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Opened 18 months ago
Last modified 18 months ago
#15111 assigned defect
MemoryError saving session
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| 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: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open D:/Cryo-EM/Fat_AL/YangZH/Heart_YangZH/PM1/PM1_Z10.mrc D:/Cryo-
> EM/Fat_AL/YangZH/Heart_YangZH/PM1/PM1_Z10.seg
Summary of feedback from opening D:/Cryo-
EM/Fat_AL/YangZH/Heart_YangZH/PM1/PM1_Z10.seg
---
notes | Opened PM1_Z10.mrc as #1, grid size 360,360,360, pixel 0.83, shown at
level 0.000977, step 2, values float32
Showing 2 region surfaces
Opened PM1_Z10.mrc as #2, grid size 360,360,360, pixel 0.83, shown at level
0.000977, step 2, values float32
Opened PM1_Z10.seg
Showing PM1_Z10.seg - 2 regions, 2 surfaces
> volume #1 step 1
> volume #1 level 0.00095
> volume #1 level 0.01195
> volume #1 level 0.0095
> hide #3.1 models
> show #3.1 models
> hide #3.2 models
> show #3.2 models
> hide #3.2 models
> volume #2 step 1
> volume #2 level 0.00095
> volume #2 level 0.0095
> show #3.2 models
> hide #3.2 models
> show #3.2 models
> hide #3.1 models
> show #3.1 models
> ui tool show "Color Actions"
> set bgColor white
> hide #3.2 models
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting flat
> lighting full
> lighting soft
> lighting simple
> surface dust #1 size 8.3
> surface dust #2 size 8.3
> "surface dust #2 size 1.7"
Unknown command: "surface dust #2 size 1.7"
> show #3.2 models
> hide #3.2 models
> show #3.2 models
> hide #3.2 models
> "surface dust #2 size 1.7"
Unknown command: "surface dust #2 size 1.7"
> hide #!1 models
> hide #!2 models
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!1 models
> "surface dust #1 size 1.7"
Unknown command: "surface dust #1 size 1.7"
> surface dust #1 size 8.3
> surface dust #1 size 1.7
> select clear
> hide #!1 models
> show #!3 models
> show #3.2 models
> hide #3.1 models
> show #3.1 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> close #2
> show #!3 models
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!1 models
> hide #3.1 models
> hide #3.2 models
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes true width 1
> graphics silhouettes true width 2
> lighting simple
> lighting soft
> lighting flat
> lighting shadows true intensity 0.5
> lighting simple
> graphics silhouettes true width 1
> open D:/Cryo-EM/Fat_AL/YangZH/Heart_YangZH/PM1/Heart_Yang_PM1_1layer_R10.pdb
Summary of feedback from opening D:/Cryo-
EM/Fat_AL/YangZH/Heart_YangZH/PM1/Heart_Yang_PM1_1layer_R10.pdb
---
warnings | Ignored bad PDB record found on line 42
SSBOND 1 CYS AA 22 CYS AA 89
Ignored bad PDB record found on line 43
SSBOND 2 CYS AB 22 CYS AB 89
Ignored bad PDB record found on line 44
SSBOND 3 CYS AC 22 CYS AC 89
Chain information for Heart_Yang_PM1_1layer_R10.pdb #2
---
Chain | Description
AA | No description available
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> transparency #1-2 60
> volume #1 level 0.01081
> volume #1 level 0.01049
> hide #2 models
> show #2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #3.1 models
> show #3.2 models
> volume #1 level 0.0095
> hide #2 models
> hide #!3 models
> show #2 models
> hide #2 models
> show #!3 models
> hide #!3 models
> hide #1.1 models
> show #1.1 models
> hide #!1 models
> show #!1 models
> show #2 models
> hide #2 models
> save "D:/Cryo-EM/Fat_AL/YangZH/Heart_YangZH/PM1/PM1_Model in map.cxs"
> includeMaps true
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, 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
File "msgpack\\_packer.pyx", line 285, in msgpack._cmsgpack.Packer._pack
File "stringsource", line 67, in
cfunc.to_py.__Pyx_CFunc_object____object___to_py.wrap
File "src\\_serialize.pyx", line 215, in chimerax.core._serialize._encode_ext
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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, 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
File "msgpack\\_packer.pyx", line 285, in msgpack._cmsgpack.Packer._pack
File "stringsource", line 67, in
cfunc.to_py.__Pyx_CFunc_object____object___to_py.wrap
File "src\\_serialize.pyx", line 215, in chimerax.core._serialize._encode_ext
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.
> save "D:/Cryo-EM/Fat_AL/YangZH/Heart_YangZH/PM1/PM1_model in map.cxs"
> includeMaps true
> save D:/YYX/Paper/AL/Yang_AL/Heart_Yang/PM1_topview.png width 1318 height
> 820 supersample 3 transparentBackground true
> show #2 models
> show #!3 models
> hide #!3 models
> hide #!1 models
> select add #2
756 atoms, 674 bonds, 102 residues, 1 model selected
> show sel cartoons
> show sel atoms
> hide sel cartoons
> show sel surfaces
[Repeated 1 time(s)]
> hide sel surfaces
> select clear
> hide #2.1 models
> show #2.1 models
> hide #!2 models
> show #!2 models
> close #2
> open D:/Cryo-EM/Fat_AL/YangZH/Heart_YangZH/PM1/Heart_Yang_PM1_1layer_R10.pdb
Summary of feedback from opening D:/Cryo-
EM/Fat_AL/YangZH/Heart_YangZH/PM1/Heart_Yang_PM1_1layer_R10.pdb
---
warnings | Ignored bad PDB record found on line 42
SSBOND 1 CYS AA 22 CYS AA 89
Ignored bad PDB record found on line 43
SSBOND 2 CYS AB 22 CYS AB 89
Ignored bad PDB record found on line 44
SSBOND 3 CYS AC 22 CYS AC 89
Chain information for Heart_Yang_PM1_1layer_R10.pdb #2
---
Chain | Description
AA | No description available
> show #2 target ab
> hide (#2 & (protein|nucleic)) target a
> cartoon hide #2
> show (#2 & ((protein&@ca)|(nucleic&@p))) target ab
> select add #2
756 atoms, 674 bonds, 1 pseudobond, 102 residues, 2 models selected
> show (#!2 & sel) target ab
> show (sel-residues & sidechain) target ab
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> select clear
> open D:/Cryo-EM/Fat_AL/YangZH/Heart_YangZH/PM1/Heart_Yang_PM1_3layer_R10.pdb
Chain information for Heart_Yang_PM1_3layer_R10.pdb #4
---
Chain | Description
AA AB AC | No description available
> hide #2 models
> show #4 target ab
> cartoon hide #4
> close #2
> open D:/Cryo-EM/Fat_AL/YangZH/Heart_YangZH/PM1/Heart_Yang_PM1_1layer_R9.pdb
Summary of feedback from opening D:/Cryo-
EM/Fat_AL/YangZH/Heart_YangZH/PM1/Heart_Yang_PM1_1layer_R9.pdb
---
warnings | Ignored bad PDB record found on line 42
SSBOND 1 CYS AA 22 CYS AA 89
Ignored bad PDB record found on line 43
SSBOND 2 CYS AB 22 CYS AB 89
Ignored bad PDB record found on line 44
SSBOND 3 CYS AC 22 CYS AC 89
> hide #4 models
> hide #2 models
> show #2 models
> open D:/Cryo-EM/Fat_AL/YangZH/Heart_YangZH/PM1/Heart_Yang_PM1_3layer_R9.pdb
Chain information for Heart_Yang_PM1_3layer_R9.pdb #5
---
Chain | Description
AA AB AC | No description available
> hide #5 models
> select add #2
743 atoms, 661 bonds, 100 residues, 1 model selected
> show sel cartoons
> show sel surfaces
> hide sel surfaces
> show sel cartoons
> show sel atoms
> hide sel atoms
> show sel atoms
> select clear
> hide #2.1 models
> show #2.1 models
> select add #2
743 atoms, 661 bonds, 100 residues, 1 model selected
> select subtract #2
1 model selected
> select clear
> close #2
> open D:/Cryo-EM/Fat_AL/YangZH/Heart_YangZH/PM1/Heart_Yang_PM1_1layer_R10.pdb
Summary of feedback from opening D:/Cryo-
EM/Fat_AL/YangZH/Heart_YangZH/PM1/Heart_Yang_PM1_1layer_R10.pdb
---
warnings | Ignored bad PDB record found on line 42
SSBOND 1 CYS AA 22 CYS AA 89
Ignored bad PDB record found on line 43
SSBOND 2 CYS AB 22 CYS AB 89
Ignored bad PDB record found on line 44
SSBOND 3 CYS AC 22 CYS AC 89
Chain information for Heart_Yang_PM1_1layer_R10.pdb #2
---
Chain | Description
AA | No description available
> select add #2
756 atoms, 674 bonds, 102 residues, 1 model selected
> select subtract #2
Nothing selected
> select add #2
756 atoms, 674 bonds, 102 residues, 1 model selected
> select subtract #2
Nothing selected
> close #2
> show #!3 models
> show #!1 models
> close #5
> show #4 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> hide #!1 models
> select clear
[Repeated 1 time(s)]
> select up
4 atoms, 2 bonds, 2 residues, 1 model selected
> select up
14 atoms, 14 bonds, 2 residues, 1 model selected
> select up
146 atoms, 148 bonds, 22 residues, 1 model selected
> select up
1512 atoms, 1548 bonds, 204 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!1 models
> show #!3 models
> hide #!3 models
> hide #4 models
> show #4 models
> show #!3 models
> hide #!3 models
> hide #!1 models
> select clear
> bind sel
Unknown command: bind sel
> bind
Unknown command: bind
> bound
Unknown command: bound
> select clear
> select /AA:22@SG
1 atom, 1 residue, 1 model selected
> select add /AA:89@SG
2 atoms, 2 residues, 1 model selected
> select clear
> select add #4
756 atoms, 774 bonds, 102 residues, 1 model selected
> hide #* target a
> show sel target ab
> open D:/Cryo-
> EM/Fat_AL/YangZH/Heart_YangZH/PM1/Heart_Yang_PM1_3layer_R10_pymol.pdb
Chain information for Heart_Yang_PM1_3layer_R10_pymol.pdb #2
---
Chain | Description
AA AB AC | No description available
> hide #4 models
> show #4 models
> hide #4 models
> show #2 target ab
> show #!1 models
> hide #!1 models
> save D:/Cryo-
> EM/Fat_AL/YangZH/Heart_YangZH/PM1/Heart_Yang_PM1_3layer_R10_chimeraX.pdb
> models #2 relModel #1
> select #2/AC:29
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2/AB:29
16 atoms, 14 bonds, 2 residues, 1 model selected
> select up
796 atoms, 816 bonds, 104 residues, 1 model selected
> select up
1512 atoms, 1550 bonds, 204 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select clear
> show #!1 models
> hide #!1 models
> hide #2 models
> show #2 models
> select clear
> select add #1
2 models selected
> select subtract #1
Nothing selected
> select add #2
756 atoms, 775 bonds, 102 residues, 1 model selected
> ui tool show "Color Actions"
No target buttons for the coloring action are checked
[Repeated 5 time(s)]
> select clear
[Repeated 2 time(s)]
> cartoon hide #2
> select clear
[Repeated 1 time(s)]
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
398 atoms, 408 bonds, 52 residues, 1 model selected
> select up
756 atoms, 775 bonds, 102 residues, 1 model selected
> color #2 white
> color #2 #ee77aaff
> color #2 #e7aac3ff
> ui tool show "Color Actions"
No target buttons for the coloring action are checked
> color sel byhetero target acs
> select clear
> show #!3 models
> hide #!3 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> hide #2 models
> show #2 models
> show #!1 models
> hide #!1 models
Volume zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.
> select add #1
2 models selected
> select add #2
756 atoms, 775 bonds, 102 residues, 3 models selected
> show #!1 models
> volume zone #1 nearAtoms sel & #2 range 4.98
> volume zone #1 nearAtoms sel & #2 range 2
> select clear
> select add #1
2 models selected
> transparency #1.1 80
> select clear
> save "D:/Cryo-EM/Fat_AL/YangZH/Heart_YangZH/PM1/PM1_model in map.cxs"
> includeMaps true
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, 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
File "msgpack\\_packer.pyx", line 285, in msgpack._cmsgpack.Packer._pack
File "stringsource", line 67, in
cfunc.to_py.__Pyx_CFunc_object____object___to_py.wrap
File "src\\_serialize.pyx", line 215, in chimerax.core._serialize._encode_ext
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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, 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
File "msgpack\\_packer.pyx", line 285, in msgpack._cmsgpack.Packer._pack
File "stringsource", line 67, in
cfunc.to_py.__Pyx_CFunc_object____object___to_py.wrap
File "src\\_serialize.pyx", line 215, in chimerax.core._serialize._encode_ext
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.
> save "D:/Cryo-EM/Fat_AL/YangZH/Heart_YangZH/PM1/PM1_model in map.cxs"
> includeMaps true
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, 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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, 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.
> show #4 models
> hide #4 models
> hide #2 models
> show #2 models
> hide #!1 models
> show #!1 models
> hide #2 models
> show #2 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> hide #2 models
> hide #!1 models
> show #4 models
> hide #4 models
> show #4 models
> close #4
> show #2 models
> show #!3 models
> show #!1 models
> hide #!1 models
> hide #2 models
> hide #!3 models
> show #!1 models
> show #2 models
> save "D:/Cryo-EM/Fat_AL/YangZH/Heart_YangZH/PM1/PM1_model in map.cxs"
> includeMaps true
> hide #2 models
> select #1
2 models selected
> color #1.1 light gray
> transparency #1.1 80
> select clear
> show #2 models
> lighting simple
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes true width 0.3
> graphics silhouettes true width 3
> graphics silhouettes true width 1
> graphics silhouettes true width 2
> graphics silhouettes true width 1
> select clear
[Repeated 1 time(s)]
> select #1
2 models selected
> hide #2 models
> show #2 models
> hide #!1 models
> select clear
[Repeated 2 time(s)]
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
398 atoms, 408 bonds, 52 residues, 1 model selected
> select up
756 atoms, 775 bonds, 102 residues, 1 model selected
> size sel stickRadius 0.3
Changed 775 bond radii
> select clear
> show #!1 models
> show #!3 models
> hide #!3 models
> hide #!1 models
> show #!1 models
> hide #1.1 models
> show #1.1 models
> hide #!1 models
> show #!1 models
> show #!3 models
> hide #!3 models
> open D:/Cryo-EM/Fat_AL/YangZH/Heart_YangZH/PM1/PM1_extradensity_Z10.mrc
Opened PM1_extradensity_Z10.mrc as #4, grid size 360,360,360, pixel 0.83,
shown at level 0.000563, step 2, values float32
> volume #4 step 1
> volume #4 level 0.0095
> select add #4
2 models selected
> surface dust #4 size 8.3
> surface dust #4 size 1.7
> select clear
Segmenting PM1_extradensity_Z10.mrc, density threshold 0.009500
Showing 22 region surfaces
137 watershed regions, grouped to 22 regions
Showing PM1_extradensity_Z10.seg - 22 regions, 22 surfaces
Segmenting PM1_extradensity_Z10.mrc, density threshold 0.009500
Showing 22 region surfaces
137 watershed regions, grouped to 22 regions
Showing PM1_extradensity_Z10.seg - 22 regions, 22 surfaces
> select clear
> select #3.1
1 model selected
Ungrouped to 3 regions
> select clear
> select #3.10
1 model selected
Ungrouped to 3 regions
> select clear
> select #3.9
1 model selected
Ungrouped to 3 regions
> select #3.19
1 model selected
> select add #3.26
2 models selected
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #2 models
> show #2 models
> hide #1.1 models
> show #1.1 models
> hide #!1 models
> show #!1 models
> select #3.12
1 model selected
Ungrouped to 2 regions
> select clear
> select #3.30
1 model selected
> select add #3.19
2 models selected
Grouped 2 regions
> select clear
> select #3.23
1 model selected
> select #3.24
1 model selected
Ungrouped to 4 regions
> select clear
> select #3.23
1 model selected
> select add #3.26
2 models selected
> select clear
> open D:/Cryo-EM/Fat_AL/YangZH/Heart_YangZH/PM1/PM1_Z10.mrc
Opened PM1_Z10.mrc as #5, grid size 360,360,360, pixel 0.83, shown at level
0.000977, step 2, values float32
> volume #5 level 0.0095
> volume #5 step 1
> select add #5
2 models selected
> transparency #5.1 60
> select clear
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #2 models
> show #2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #2 models
> show #2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> select #3.26
1 model selected
> select add #3.23
2 models selected
Grouped 2 regions
> color #3.23 orange
> select clear
> select #3.5
1 model selected
Ungrouped to 2 regions
> select clear
> select #3.26
1 model selected
Ungrouped to 2 regions
> select clear
> hide #!3 models
> show #!3 models
> select clear
> select #3.33
1 model selected
> select #3.24
1 model selected
Ungrouped to 2 regions
> select clear
> select #3.33
1 model selected
> select #3.5
1 model selected
Ungrouped to 3 regions
> select clear
> select #3.35
1 model selected
Ungrouped to 0 regions
> select clear
> select #3.35
1 model selected
Ungrouped to 0 regions
> select #3.35
1 model selected
Ungrouped to 0 regions
> select clear
> select #3.33
1 model selected
> select #3.4
1 model selected
Ungrouped to 2 regions
> select clear
> select #3.5
1 model selected
Ungrouped to 2 regions
> select clear
> select #3.4
1 model selected
Ungrouped to 3 regions
> select clear
> select #3.40
1 model selected
> select add #3.33
2 models selected
> select add #3.23
3 models selected
Grouped 3 regions
> color #3.4 orange
> select clear
> hide #!4 models
> show #!4 models
> hide #!3 models
> select clear
> show #!3 models
> select #3.6
1 model selected
Ungrouped to 4 regions
> select clear
> select #3.23
1 model selected
> select add #3.4
2 models selected
Grouped 2 regions
> color #3.4 orange
> select clear
> select #3.13
1 model selected
> select add #3.16
2 models selected
> select clear
> select #5
2 models selected
> select clear
> select #3.16
1 model selected
Ungrouped to 2 regions
> select clear
> select #3.23
1 model selected
> select add #3.13
2 models selected
> select add #3.4
3 models selected
Grouped 3 regions
> color #3.4 orange
> select clear
> select #3.8
1 model selected
Ungrouped to 3 regions
> select clear
> select #3.23
1 model selected
Ungrouped to 3 regions
> select clear
> select #3.8
1 model selected
> select add #3.43
2 models selected
> select add #3.4
3 models selected
Grouped 3 regions
> select clear
> select #3.12
1 model selected
> select add #3.4
2 models selected
Grouped 2 regions
> color #3.4 orange
> select clear
[Repeated 1 time(s)]
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!3 models
> show #!3 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> select #3.20
1 model selected
Ungrouped to 2 regions
> select #3.12
1 model selected
> select add #3.4
2 models selected
Grouped 2 regions
> color #3.4 orange
> select clear
> select #3.4
1 model selected
Opened PM1_extradensity_Z10_imasked as #6, grid size 360,360,360, pixel 0.83,
shown at step 1, values float32
> hide #!6 models
> hide #!3 models
> show #!6 models
> hide #1.1 models
> hide #2 models
> show #2 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!6 models
> show #!6 models
> close #6
> show #!5 models
> hide #!5 models
> show #!4 models
> show #!3 models
> hide #!4 models
Opened PM1_extradensity_Z10_imasked as #6, grid size 360,360,360, pixel 0.83,
shown at step 1, values float32
> hide #!6 models
> hide #2 models
> hide #!3 models
> show #!6 models
> show #!3 models
> hide #!3 models
> show #2 models
> show #!1 models
> show #1.1 models
> select #6
2 models selected
> color #6.1 orange
> select clear
[Repeated 1 time(s)]
> save D:/Cryo-EM/Fat_AL/YangZH/Heart_YangZH/PM1/PM1_extradensity_1layer.mrc
> models #6
> save "D:/Cryo-EM/Fat_AL/YangZH/Heart_YangZH/PM1/PM1_model in map.cxs"
> includeMaps true
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, 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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, 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 "D:/Cryo-EM/Fat_AL/YangZH/Heart_YangZH/PM1/PM1_model in map.cxs"
> includeMaps true
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 136, in write
self._f.write(buf)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\lz4\frame\\__init__.py",
line 740, in write
compressed = self._compressor.compress(data)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\lz4\frame\\__init__.py",
line 258, in compress
result = compress_chunk(
MemoryError
MemoryError
File "C:\Program Files\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 136, in write
self._f.write(buf)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\lz4\frame\\__init__.py",
line 740, in write
compressed = self._compressor.compress(data)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\lz4\frame\\__init__.py",
line 258, in compress
result = compress_chunk(
MemoryError
MemoryError
File "C:\Program Files\ChimeraX\bin\lib\site-packages\lz4\frame\\__init__.py",
line 258, in compress
result = compress_chunk(
See log for complete Python traceback.
> save "D:/Cryo-EM/Fat_AL/YangZH/Heart_YangZH/PM1/PM1_model in map.cxs"
> includeMaps true
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, 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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, 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.
> hide #!6 models
> show #!6 models
> hide #2 models
> show #2 models
> hide #!1 models
> show #!1 models
> save "D:/YYX/Paper/AL/Yang_AL/Heart_Yang/PM1_model in map.png" width 1318
> height 820 supersample 3 transparentBackground true
> open D:/Cryo-
> EM/Fat_AL/YangZH/Heart_YangZH/PM1/Heart_Yang_PM1_3layer_R10_chimeraX.pdb
Chain information for Heart_Yang_PM1_3layer_R10_chimeraX.pdb #7
---
Chain | Description
AA AB AC | No description available
> hide #7 models
> show #7 models
> hide #!1 models
> hide #2 models
> select #7/AC:12
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add #7/AB:106
13 atoms, 11 bonds, 2 residues, 1 model selected
> select up
97 atoms, 97 bonds, 14 residues, 1 model selected
> select up
1512 atoms, 1550 bonds, 204 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #2 models
> hide #2 models
> select add #7
756 atoms, 775 bonds, 102 residues, 1 model selected
> show sel target ab
> cartoon hide sel
> select clear
> show #!1 models
> hide #!1 models
> show #!1 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> close #2
> save "D:/Cryo-EM/Fat_AL/YangZH/Heart_YangZH/PM1/PM1_model in map.cxs"
> includeMaps true
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, 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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, 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.
> hide #7 models
> show #7 models
> hide #!1 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
64 atoms, 63 bonds, 9 residues, 1 model selected
> select up
756 atoms, 775 bonds, 102 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #ee77aaff target acs
> color sel #e7aac3ff target acs
> color sel #ffffffff target acs
> color sel #ee77aaff target acs
> color sel #e7aac3ff target acs
> color sel byhetero
> set sel stickRadius 0.3
Expected keyword "selectionColor" or "selectionWidth"
> size sel stickRadius 0.3
Changed 775 bond radii
> select clear
> show #!1 models
> save "D:/Cryo-EM/Fat_AL/YangZH/Heart_YangZH/PM1/PM1_model in map2.cxs"
> includeMaps true
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, 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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, 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.
OpenGL version: 3.3.0 NVIDIA 474.64
OpenGL renderer: NVIDIA GeForce GT 730/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: zh_CN.cp936
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows
Manufacturer: LENOVO
Model: 90L0CTO1WW
OS: Microsoft Windows 10 企业版 (Build 19045)
Memory: 17,110,429,696
MaxProcessMemory: 137,438,953,344
CPU: 12 AMD Ryzen 5 3600 6-Core Processor
OSLanguage: zh-CN
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2022.9.24
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
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-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
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: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
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
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
comtypes: 1.1.10
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
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: 2022.6
pywin32: 303
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
WMI: 1.5.1
zipp: 3.11.0
Change History (1)
comment:1 by , 18 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Sessions |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → MemoryError saving session |
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