MemoryError saving session after many 'vop zone' commands

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19044
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open E:\\\实验室\\\其它\\\14-课题整理\\\文章写作\\\数据整理\\\Helix\\\ligand-1.cxs

Opened J1170_UDP_galactose_sharp.mrc as #2, grid size 384,384,384, pixel 1.1,
shown at level 0.2, step 1, values float32  
Opened J1170_UDP_galactose_sharp.mrc zone as #3, grid size 384,384,384, pixel
1.1, shown at level 0.2, step 1, values float32  
Opened J1170_UDP_galactose_sharp.mrc zone as #4, grid size 384,384,384, pixel
1.1, shown at level 0.2, step 1, values float32  
Opened J1170_UDP_galactose_sharp.mrc zone as #5, grid size 384,384,384, pixel
1.1, shown at level 0.2, step 1, values float32  
Opened J1170_UDP_galactose_sharp.mrc zone as #6, grid size 384,384,384, pixel
1.1, shown at level 0.2, step 1, values float32  
Opened J1170_UDP_galactose_sharp.mrc zone as #7, grid size 384,384,384, pixel
1.1, shown at level 0.2, step 1, values float32  
Opened J1170_UDP_galactose_sharp.mrc zone as #8, grid size 384,384,384, pixel
1.1, shown at level 0.2, step 1, values float32  
Opened J1170_UDP_galactose_sharp.mrc zone as #9, grid size 384,384,384, pixel
1.1, shown at level 0.2, step 1, values float32  
Log from Fri Mar 1 10:35:41 2024 Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open E:\\\实验室\\\其它\\\14-课题整理\\\文章写作\\\数据整理\\\Helix\\\PLO-
> COL_J1170-ABUV-039-coot-3rd.pdb

Chain information for PLO-COL_J1170-ABUV-039-coot-3rd.pdb #1  
---  
Chain | Description  
A B | No description available  
U V | No description available  
  

> open
> E:\\\实验室\\\其它\\\14-课题整理\\\文章写作\\\数据整理\\\Helix\\\J1170_UDP_galactose_sharp.mrc

Opened J1170_UDP_galactose_sharp.mrc as #2, grid size 384,384,384, pixel 1.1,
shown at level 0.168, step 2, values float32  

> volume #2 step 1

> set bgColor white

> surface dust #2 size 11

> fitmap #1 inMap #2

Fit molecule PLO-COL_J1170-ABUV-039-coot-3rd.pdb (#1) to map
J1170_UDP_galactose_sharp.mrc (#2) using 20968 atoms  
average map value = 0.7349, steps = 48  
shifted from previous position = 0.0362  
rotated from previous position = 0.0453 degrees  
atoms outside contour = 524, contour level = 0.16777  
  
Position of PLO-COL_J1170-ABUV-039-coot-3rd.pdb (#1) relative to
J1170_UDP_galactose_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999975 0.00010916 0.00069553 -0.15080643  
-0.00010941 0.99999993 0.00036115 -0.06983153  
-0.00069549 -0.00036122 0.99999969 0.25366731  
Axis -0.45645586 0.87896075 -0.13811606  
Axis point 359.15309264 0.00000000 235.05042989  
Rotation angle (degrees) 0.04533715  
Shift along axis -0.02757823  
  

> color red

> color byhetero

> hide atoms

> volume hide

> hide cartoons

> select #1/B:337-353

146 atoms, 153 bonds, 17 residues, 1 model selected  

> vop zone #2 near sel range 1.7 newmap 1

Opened J1170_UDP_galactose_sharp.mrc zone as #3, grid size 384,384,384, pixel
1.1, shown at step 1, values float32  

> hide sel atoms

> volume #!3 hide

> select ::name="AKG"

20 atoms, 18 bonds, 2 residues, 1 model selected  

> show sel atoms

> select clear

Drag select of 10 atoms, 9 bonds  

> name frozen B-AKG sel

> hide sel atoms

> select clear

> hide atoms

> select ::name="FE2"

2 atoms, 2 residues, 1 model selected  

> show sel atoms

> select clear

Drag select of 1 atoms  

> name frozen B-FE sel

> select clear

> hide atoms

> select ::name="MN"

2 atoms, 2 residues, 1 model selected  

> show sel atoms

> select clear

Drag select of 1 atoms  

> name frozen B-MN sel

> select clear

> hide atoms

> select ::name="NAG"

126 atoms, 130 bonds, 9 residues, 1 model selected  

> show sel atoms

> select clear

Drag select of 28 atoms, 29 bonds  

> name frozen B-NAG-1 sel

> select clear

Drag select of 14 atoms, 14 bonds  

> name frozen B-NAG-2 sel

> select clear

> hide atoms

> select ::name="UDP"

50 atoms, 52 bonds, 2 residues, 1 model selected  

> show sel atoms

> select clear

Drag select of 25 atoms, 26 bonds  

> name frozen B-UDP sel

> select clear

> hide atoms

> save E:/实验室/其它/14-课题整理/文章写作/数据整理/Helix/ligand.cxs

> select B-AKG

10 atoms, 9 bonds, 1 residue, 1 model selected  

> vop zone #2 near sel range 1.7 newmap 1

Opened J1170_UDP_galactose_sharp.mrc zone as #4, grid size 384,384,384, pixel
1.1, shown at step 1, values float32  

> volume #!4 hide

> hide sel atoms

> select B-FE

1 atom, 1 residue, 1 model selected  

> vop zone #2 near sel range 1.7 newmap 1

Opened J1170_UDP_galactose_sharp.mrc zone as #5, grid size 384,384,384, pixel
1.1, shown at step 1, values float32  

> hide sel atoms

> volume #!5 hide

> select B-MN

1 atom, 1 residue, 1 model selected  

> vop zone #2 near sel range 1.7 newmap 1

Opened J1170_UDP_galactose_sharp.mrc zone as #6, grid size 384,384,384, pixel
1.1, shown at step 1, values float32  

> hide sel atoms

> volume #!6 hide

> select B-NAG-1

28 atoms, 29 bonds, 2 residues, 1 model selected  

> vop zone #2 near sel range 1.7 newmap 1

Opened J1170_UDP_galactose_sharp.mrc zone as #7, grid size 384,384,384, pixel
1.1, shown at step 1, values float32  

> hide sel atoms

> volume #!7 hide

> select B-NAG-2

14 atoms, 14 bonds, 1 residue, 1 model selected  

> vop zone #2 near sel range 1.7 newmap 1

Opened J1170_UDP_galactose_sharp.mrc zone as #8, grid size 384,384,384, pixel
1.1, shown at step 1, values float32  

> hide sel atoms

> volume #!8 hide

> select B-UDP

25 atoms, 26 bonds, 1 residue, 1 model selected  

> vop zone #2 near sel range 1.7 newmap 1

Opened J1170_UDP_galactose_sharp.mrc zone as #9, grid size 384,384,384, pixel
1.1, shown at step 1, values float32  

> hide sel atoms

> volume #!9 hide

> color #3 black models

> color #3-9 black models

> show #!4 models

> hide #!4 models

> show #!3 models

> volume #!3 style mesh

> hide #!3 models

> show #!4 models

> hide sel cartoons

> volume #!4 style mesh

> hide #!4 models

> show #!3 models

> volume all level 0.2

> show #!9 models

> hide #!9 models

> show #!8 models

> hide #!8 models

> show #!7 models

> hide #!7 models

> show #!4 models

> save E:/实验室/其它/14-课题整理/文章写作/数据整理/Helix/ligand-1.cxs

——— End of log from Fri Mar 1 10:35:41 2024 ———

opened ChimeraX session  

> close #4-9

> hide #!3 models

> show #1/B:362-364

> vop zone #2 near sel range 1.7 newmap 1

Opened J1170_UDP_galactose_sharp.mrc zone as #4, grid size 384,384,384, pixel
1.1, shown at step 1, values float32  

> hide sel atoms

> select clear

> hide atoms

> close #4

> show #1/B:362-364

> vop zone #2 near sel range 1.7 newmap 1

no atoms specified for zone  

> hide atoms

> select #1/B:362-364

25 atoms, 25 bonds, 3 residues, 1 model selected  

> select #1/B:362-364

25 atoms, 25 bonds, 3 residues, 1 model selected  

> vop zone #2 near sel range 1.7 newmap 1

Opened J1170_UDP_galactose_sharp.mrc zone as #4, grid size 384,384,384, pixel
1.1, shown at step 1, values float32  

> volume #!4 hide

> hide sel atoms

> select #1/B:368-380

98 atoms, 98 bonds, 13 residues, 1 model selected  

> vop zone #2 near sel range 1.7 newmap 1

Opened J1170_UDP_galactose_sharp.mrc zone as #5, grid size 384,384,384, pixel
1.1, shown at step 1, values float32  

> volume #!5 hide

> select #1/B:402-409

68 atoms, 67 bonds, 8 residues, 1 model selected  

> vop zone #2 near sel range 1.7 newmap 1

Opened J1170_UDP_galactose_sharp.mrc zone as #6, grid size 384,384,384, pixel
1.1, shown at step 1, values float32  

> volume #!6 hide

> select #1/B:444-448

43 atoms, 43 bonds, 5 residues, 1 model selected  

> vop zone #2 near sel range 1.7 newmap 1

Opened J1170_UDP_galactose_sharp.mrc zone as #7, grid size 384,384,384, pixel
1.1, shown at step 1, values float32  

> volume #!7 hide

> select #1/B:469-474

46 atoms, 45 bonds, 6 residues, 1 model selected  

> vop zone #2 near sel range 1.7 newmap 1

Opened J1170_UDP_galactose_sharp.mrc zone as #8, grid size 384,384,384, pixel
1.1, shown at step 1, values float32  

> volume #!8 hide

> select #1/B:489-500

99 atoms, 101 bonds, 12 residues, 1 model selected  

> vop zone #2 near sel range 1.7 newmap 1

Opened J1170_UDP_galactose_sharp.mrc zone as #9, grid size 384,384,384, pixel
1.1, shown at step 1, values float32  

> volume #!9 hide

> select #1/B:528-531

37 atoms, 39 bonds, 4 residues, 1 model selected  

> vop zone #2 near sel range 1.7 newmap 1

Opened J1170_UDP_galactose_sharp.mrc zone as #10, grid size 384,384,384, pixel
1.1, shown at step 1, values float32  

> volume #!10 hide

> select #1/B:537-544

75 atoms, 78 bonds, 8 residues, 1 model selected  

> vop zone #2 near sel range 1.7 newmap 1

Opened J1170_UDP_galactose_sharp.mrc zone as #11, grid size 384,384,384, pixel
1.1, shown at step 1, values float32  

> volume #!11 hide

> select #1/B:549-554

51 atoms, 51 bonds, 6 residues, 1 model selected  

> vop zone #2 near sel range 1.7 newmap 1

Opened J1170_UDP_galactose_sharp.mrc zone as #12, grid size 384,384,384, pixel
1.1, shown at step 1, values float32  

> volume #!12 hide

> select #1/B:574-587

117 atoms, 118 bonds, 14 residues, 1 model selected  

> vop zone #2 near sel range 1.7 newmap 1

Opened J1170_UDP_galactose_sharp.mrc zone as #13, grid size 384,384,384, pixel
1.1, shown at step 1, values float32  

> volume #!13 hide

> hide sel atoms

> select #1/B:614-617

33 atoms, 32 bonds, 4 residues, 1 model selected  

> vop zone #2 near sel range 1.7 newmap 1

Opened J1170_UDP_galactose_sharp.mrc zone as #14, grid size 384,384,384, pixel
1.1, shown at step 1, values float32  

> volume #!14 hide

> select #1/B:620-630

103 atoms, 105 bonds, 11 residues, 1 model selected  

> vop zone #2 near sel range 1.7 newmap 1

Opened J1170_UDP_galactose_sharp.mrc zone as #15, grid size 384,384,384, pixel
1.1, shown at step 1, values float32  

> volume #!15 hide

> select #1/B:632-638

49 atoms, 49 bonds, 7 residues, 1 model selected  

> vop zone #2 near sel range 1.7 newmap 1

Opened J1170_UDP_galactose_sharp.mrc zone as #16, grid size 384,384,384, pixel
1.1, shown at step 1, values float32  

> close #16

> save E:/实验室/其它/14-课题整理/文章写作/数据整理/Helix/plod-2.cxs

Traceback (most recent call last):  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-packages\chimerax\core\session.py",
line 912, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-packages\chimerax\core\session.py",
line 641, in save  
fserialize(stream, data)  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-packages\chimerax\core\serialize.py",
line 76, in msgpack_serialize  
stream.write(packer.pack(obj))  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-packages\chimerax\core\safesave.py",
line 147, in write  
self._f.write(buf)  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-packages\lz4\frame\\__init__.py", line
740, in write  
compressed = self._compressor.compress(data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-packages\lz4\frame\\__init__.py", line
258, in compress  
result = compress_chunk(  
^^^^^^^^^^^^^^^  
MemoryError  
  
MemoryError  
  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-packages\lz4\frame\\__init__.py", line
258, in compress  
result = compress_chunk(  
^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-packages\chimerax\toolbar\tool.py",
line 165, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 397, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1302, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-
packages\chimerax\toolbar\\__init__.py", line 37, in run_provider  
providers.run_provider(session, name)  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-
packages\chimerax\toolbar\providers.py", line 56, in run_provider  
what(session)  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-
packages\chimerax\toolbar\providers.py", line 38, in _file_save  
show_save_file_dialog(session)  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display  
run(session, cmd)  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\ChimeraX\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 "D:\ChimeraX\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save  
return cxs_save(session, path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-packages\chimerax\core\session.py",
line 912, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-packages\chimerax\core\session.py",
line 641, in save  
fserialize(stream, data)  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-packages\chimerax\core\serialize.py",
line 76, in msgpack_serialize  
stream.write(packer.pack(obj))  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-packages\chimerax\core\safesave.py",
line 147, in write  
self._f.write(buf)  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-packages\lz4\frame\\__init__.py", line
740, in write  
compressed = self._compressor.compress(data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-packages\lz4\frame\\__init__.py", line
258, in compress  
result = compress_chunk(  
^^^^^^^^^^^^^^^  
MemoryError  
  
MemoryError  
  
File "D:\ChimeraX\ChimeraX\bin\Lib\site-packages\lz4\frame\\__init__.py", line
258, in compress  
result = compress_chunk(  
^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 536.99
OpenGL renderer: NVIDIA GeForce RTX 4060 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: zh_CN.cp936
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: Acer
Model: Predator PHN16-71
OS: Microsoft Windows 10 专业版 (Build 19044)
Memory: 16,886,128,640
MaxProcessMemory: 137,438,953,344
CPU: 20 13th Gen Intel(R) Core(TM) i5-13500HX
OSLanguage: zh-CN

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    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-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    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: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.13
    ChimeraX-ModelPanel: 1.4
    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: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.3
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    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-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    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: 1.33.2
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.0
    comtypes: 1.1.14
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.0
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.5.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.8
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 23.2
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 10.0.1
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pywin32: 305
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.7
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.5
    sphinxcontrib-htmlhelp: 2.0.4
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.6
    sphinxcontrib-serializinghtml: 1.1.9
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.3
    urllib3: 2.1.0
    wcwidth: 0.2.12
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9
    WMI: 1.5.1

[Tom Goddard]

The session save memory errors are always in the LZ4 compressor. Maybe it is not simply streaming the compressed data to the file but instead makes a whole compressed copy in memory.

The vop zone command with "newmap 1" option is making lots of new volumes that will be saved in the session since there is no file for those maps.

[Eric Pettersen]

Are we using the default "frame" format for lz4, or instead "block" or "streaming"? Looking at the docs here: ​https://pypi.org/project/lz4/ it sounds like "frame" does make a copy and "streaming" does not, based on snippets from the page you get from clicking on the "streaming" link:

"Streaming" API : This is designed for complex things. For example, compress huge stream data in restricted memory environment."

--and--

"Streaming API doesn't keep a mirror copy of dependent (de)compressed memory"

--but--

"Experimental bindings for the the streaming format specification are also included, but further work on those is required."

[Tom Goddard]

ChimeraX session compression uses PyPi lz4 module lz4.frame.open() as shown below from core/session.py. So maybe a switch to streaming would avoid these memory errors.

            def lz4_open(path):
                import lz4.frame
                f = SaveFile(path, open=lambda path: lz4.frame.open(path, 'wb'))
                return f