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Opened 8 months ago
Closed 8 months ago
#16941 closed defect (limitation)
ArrayMemoryError saving session with maps
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19045
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
You can double click a model's Name or ID in the model panel to edit those
fields
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:/YYX/data/Mice_amyloid/Model/5FAD_6M_Female/Type3/job175/postprocess_masked.mrc
Opened postprocess_masked.mrc as #1, grid size 288,288,288, pixel 0.83, shown
at level 0.0169, step 2, values float32
> open
> D:/YYX/data/Mice_amyloid/Model/5FAD_6M_Female/Type3/postprocess_masked.mrc
Opened postprocess_masked.mrc as #2, grid size 288,288,288, pixel 0.83, shown
at level 0.00335, step 2, values float32
> close #1
> rename #2 5fad_Type3
> volume #2 step 1
> volume #2 level 0.1
> volume #2 level 0.001
> volume #2 level 0.01401
> ui tool show "Color Actions"
> set bgColor white
> graphics silhouettes true
> color white target acs
> open D:/YYX/data/Mice_amyloid/Model/5FAD_6M_Female/Type3/Type3_3layer_R2.pdb
Chain information for Type3_3layer_R2.pdb #1
---
Chain | Description
A B C D E F | No description available
> style stick
Changed 2982 atom styles
> transparency 80
> transparency 90
> transparency 80
> hide #!2 models
Drag select of 50 atoms, 52 bonds
> select up
59 atoms, 53 bonds, 11 residues, 1 model selected
> select up
150 atoms, 147 bonds, 11 residues, 1 model selected
> select up
208 atoms, 206 bonds, 16 residues, 1 model selected
> select up
994 atoms, 1002 bonds, 66 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 43 atoms, 44 bonds
> select up
54 atoms, 47 bonds, 8 residues, 1 model selected
> select up
108 atoms, 104 bonds, 8 residues, 1 model selected
> select up
181 atoms, 179 bonds, 14 residues, 1 model selected
> select up
994 atoms, 1002 bonds, 66 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!2 models
> hide #1 models
> show #1 models
> hide #!2 models
> select add #1
994 atoms, 1002 bonds, 66 residues, 1 model selected
> hide H
> select clear
Drag select of 485 atoms, 494 bonds
> color sel royal blue target acs
> select clear
> select add #1
994 atoms, 1002 bonds, 66 residues, 1 model selected
> color sel royal blue target acs
> color sel dodger blue target acs
> color sel byhetero target acs
> select clear
> show #!2 models
> volume zone #2 nearAtoms #1 range 4.98
> volume zone #2 nearAtoms #1 range 2
> volume #2 level 0.02153
[Repeated 1 time(s)]
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> volume #2 level 0.01668
> select add #1
994 atoms, 1002 bonds, 66 residues, 1 model selected
> volume zone #2 nearAtoms sel & #1 range 4.98
> volume zone #2 nearAtoms sel & #1 range 2
> volume #2 level 0.01903
> select add #2
994 atoms, 1002 bonds, 66 residues, 3 models selected
> select subtract #2
994 atoms, 1002 bonds, 66 residues, 1 model selected
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> volume #2 level 0.01683
> volume #2 region 0,0,0,287,287,287
> select clear
> volume zone #2 nearAtoms #1 range 4.98
> volume zone #2 nearAtoms #1 range 2
> select clear
> volume #2 level 0.01856
> select add #1
994 atoms, 1002 bonds, 66 residues, 1 model selected
> set sel stickRadius 2
Expected keyword "selectionColor" or "selectionWidth"
> set stickRadius 2set sel stickRadius 2
Expected a keyword
> set stickRadius 2
Expected a keyword
> set size stickRadius 2
Expected a keyword
> size stickRadius 2
Changed 1002 bond radii
> size stickRadius 0.5
Changed 1002 bond radii
> size stickRadius 0.3
Changed 1002 bond radii
> select clear
> volume #2 level 0.01997
> volume #2 level 0.01887
> select add #2
2 models selected
> select subtract #2
Nothing selected
> select add #2
2 models selected
> select subtract #2
Nothing selected
> select add #1
994 atoms, 1002 bonds, 66 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #2
2 models selected
> select subtract #2
Nothing selected
> select add #2
2 models selected
> select subtract #2
Nothing selected
> select add #2
2 models selected
> select subtract #2
Nothing selected
> combine #2
No structures specified
> select add #2
2 models selected
> combine #2
No structures specified
> combine #2 bring to #3
Expected a keyword
> combine #2 to #3
Expected a keyword
> combine sel
No structures specified
> select subtract #2
Nothing selected
> select add #2
2 models selected
> select subtract #2
Nothing selected
> select add #2
2 models selected
> select subtract #2
Nothing selected
> select add #1
994 atoms, 1002 bonds, 66 residues, 1 model selected
> select add #2
994 atoms, 1002 bonds, 66 residues, 3 models selected
> volume sel region all imageMode "full region"
> volume unzone sel
> mousemode rightMode "crop volume"
> volume #2 level 0.01589
> select clear
> volume #2 level 0.01636
> open D:/YYX/data/Mice_amyloid/Model/5FAD_6M_Female/Type3/Type3_3layer_R2.pdb
Chain information for Type3_3layer_R2.pdb #3
---
Chain | Description
A B C D E F | No description available
> style stick
Changed 3976 atom styles
> hide #1 models
> select add #3
2982 atoms, 3006 bonds, 198 residues, 1 model selected
> color sel cornflower blue
> color sel byhetero
> hide H
> select clear
> size sel stickRadius 0.3
Changed 0 bond radii
> select add #3
2982 atoms, 3006 bonds, 198 residues, 1 model selected
> size sel stickRadius 0.3
Changed 3006 bond radii
> select clear
> size sel stickRadius 0.2
Changed 0 bond radii
> select add #3
2982 atoms, 3006 bonds, 198 residues, 1 model selected
> size sel stickRadius 0.2
Changed 3006 bond radii
> select clear
> select add #3
2982 atoms, 3006 bonds, 198 residues, 1 model selected
> size sel stickRadius 0.25
Changed 3006 bond radii
> select clear
> open
> D:/YYX/data/Mice_amyloid/Model/5FAD_6M_Female/Type2/job195/postprocess_masked.mrc
Opened postprocess_masked.mrc as #4, grid size 288,288,288, pixel 0.83, shown
at level 0.0009, step 2, values float32
> volume #4 level 0.01037
> hide #3 models
> hide #!2 models
> volume #4 step 1
> select add #4
2 models selected
> surface dust #4 size 8.3
> surface dust #4 size 3
> surface dust #4 size 5
> select clear
> rename #4 5fad_Type2
> select add #4
2 models selected
> color sel white target acs
> transparency #4.1 80
> select clear
> open
> D:/YYX/data/Mice_amyloid/Model/5FAD_6M_Female/Type2/PHENIX/RealSpaceRefine_2/5FAD_Type2_3layer_R2_real_space_refined.pdb
Chain information for 5FAD_Type2_3layer_R2_real_space_refined.pdb #5
---
Chain | Description
A B C D E F | No description available
> style #5 stick
Changed 1356 atom styles
> select add #5
1356 atoms, 1374 bonds, 186 residues, 1 model selected
> size sel stickRadius 0.25
Changed 1374 bond radii
> color sel orange red target acs
> color sel orange target acs
> color sel byhetero target acs
> select clear
> hide #5 models
> hide #!4 models
> open D:/YYX/data/Mice_amyloid/Model/ApoE4/job135/postprocess_masked.mrc
Opened postprocess_masked.mrc as #6, grid size 288,288,288, pixel 0.83, shown
at level 0.0013, step 2, values float32
> rename #6 5Fad_ApoE4
> volume #6 step 1
> volume #6 level 0.01002
> volume #6 level 0.01227
> select add #6
2 models selected
> color sel white target acs
> transparency #6.1 80
> select clear
> open
> D:/YYX/data/Mice_amyloid/Model/ApoE4/PHENIX/RealSpaceRefine_2/ApoE4_Type2_3layer_R1_real_space_refined.pdb
Chain information for ApoE4_Type2_3layer_R1_real_space_refined.pdb #7
---
Chain | Description
A B C D E F | No description available
> select add #7
1356 atoms, 1374 bonds, 186 residues, 1 model selected
> style sel stick
Changed 1356 atom styles
> size sel stickRadius 0.25
Changed 1374 bond radii
> color sel green target acs
> color sel forest green target acs
> color sel byhetero target acs
> select clear
> select add #7
1356 atoms, 1374 bonds, 186 residues, 1 model selected
> color sel sea green target acs
> color sel byhetero target acs
> color sel green target acs
> color sel byhetero target acs
> color sel forest green target acs
> color sel byhetero target acs
> select clear
> select add #7
1356 atoms, 1374 bonds, 186 residues, 1 model selected
> color sel green target acs
> color sel byhetero target acs
> select clear
> volume #6 level 0.00915
> show #5 models
> show #!4 models
> hide #7 models
> hide #!6 models
> select add #4
2 models selected
> select subtract #4
Nothing selected
> volume #4 level 0.009144
> volume #4 level 0.009602
> hide #5 models
> hide #!4 models
> show #!6 models
> show #5 models
> show #!4 models
> hide #!6 models
> hide #!4 models
> hide #5 models
> show #7 models
> show #!6 models
> save "D:/YYX/data/Mice_amyloid/Model/Mouse model.cxs" includeMaps true
> hide #!6 models
> hide #7 models
> show #5 models
> show #!4 models
> hide #!4 models
> show #!4 models
> open
> D:/YYX/data/Mice_amyloid/Model/5FAD_6M_Female/Type2/job195/postprocess_masked.mrc
Opened 5fad_Type2 as #8, grid size 288,288,288, pixel 0.83, shown at level
0.0009, step 2, values float32
> select add #8
2 models selected
> volume #8 level 0.01051
> volume #8 step 1
> volume #8 level 0.01271
> hide #!4 models
> show #!6 models
> hide #!6 models
> show #1 models
> hide #1 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #5 models
> hide #!4 models
> close #8
> show #1 models
> hide #1 models
> show #!2 models
> show #3 models
> select add #3
2982 atoms, 3006 bonds, 198 residues, 1 model selected
> select subtract #3
Nothing selected
> select add #1
994 atoms, 1002 bonds, 66 residues, 1 model selected
> select subtract #1
Nothing selected
> show #1 models
> hide #1 models
> hide #!2 models
> show #!2 models
> volume #2 level 0.01448
> hide #!2 models
> hide #3 models
> show #!4 models
> show #5 models
> volume #4 level 0.009144
> surface dust #4 size 8.3
> surface dust #4 size 0
> volume #4 level 0.01342
> volume #4 level 0.01418
> volume #4 region 0,0,0,287,287,287
> show #!6 models
> hide #5 models
> show #7 models
> hide #!4 models
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "C:\Program Files\ChimeraX\bin\lib\json\\__init__.py", line 180, in dump
fp.write(chunk)
OSError: [Errno 28] No space left on device
During handling of the above exception, another exception occurred:
OSError: [Errno 28] No space left on device
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 350, in _command_started_cb
self.history_dialog.add(self._just_typed_command or cmd_text,
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 452, in add
self._history.enqueue((item, typed))
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 171, in enqueue
self.save()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 201, in save
self._history.save(self._queue)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\history.py", line 109, in save
json.dump(obj, f, ensure_ascii=False)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 85, in __exit__
self._f.close()
OSError: [Errno 28] No space left on device
Error processing trigger "command started":
OSError: [Errno 28] No space left on device
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 85, in __exit__
self._f.close()
See log for complete Python traceback.
> hide #!6 models
> show #!6 models
> hide #7 models
> show #7 models
> select add #7
1356 atoms, 1374 bonds, 186 residues, 1 model selected
> select subtract #7
Nothing selected
> volume #6 level 0.009524
> hide #7 models
> show #7 models
> hide #!6 models
> show #!6 models
> show #!4 models
> hide #!4 models
> show #3 models
> hide #3 models
> rename #4 5fad_Type2_P21
> open
> D:/YYX/data/Mice_amyloid/Model/5FAD_6M_Female/Type2/job153/postprocess_masked.mrc
Opened postprocess_masked.mrc as #8, grid size 288,288,288, pixel 0.83, shown
at level 0.000903, step 2, values float32
> rename #8 5fad_Type2_C1
> volume #8 step 1
> hide #!6 models
> hide #7 models
> volume #8 level 0.008596
> open D:/YYX/data/Mice_amyloid/Model/emd_13809.map.mrc
MRC header value nsymbt (-816136225) is invalid
> open D:/YYX/data/Mice_amyloid/Model/emd_13809.mrc
Opened emd_13809.mrc as #9, grid size 256,256,256, pixel 0.73, shown at level
0.00605, step 1, values float32
> close #9
> save "D:/YYX/data/Mice_amyloid/Model/Mouse model.cxs" includeMaps true
> open
> D:/YYX/data/Mice_amyloid/Model/5FAD_6M_Female/Type2/PHENIX/RealSpaceRefine_5/5FAD_Type2_3layer_C1_R2_real_space_refined.pdb
Chain information for 5FAD_Type2_3layer_C1_R2_real_space_refined.pdb #9
---
Chain | Description
A B C D E F | No description available
> select add #8
2 models selected
> volume #8 color white
> transparency #8.1 80
> style #9 stick
Changed 1356 atom styles
> hide #!8 models
> select add #9
1356 atoms, 1374 bonds, 186 residues, 3 models selected
> ui tool show "Color Actions"
> color sel orange red target acs
> color sel orange target acs
> show #!8 models
> color #8 #ffffff33 models
> select subtract #9
2 models selected
> select subtract #8
Nothing selected
> select add #9
1356 atoms, 1374 bonds, 186 residues, 1 model selected
> color sel byhetero target acs
> select subtract #9
Nothing selected
> select add #9
1356 atoms, 1374 bonds, 186 residues, 1 model selected
> size sel stickRadius 2.5
Changed 1374 bond radii
> size sel stickRadius 0.25
Changed 1374 bond radii
> select clear
> volume #8 level 0.01005
> volume #8 level 0.009524
> volume #8 region 0,0,24,287,287,287
> volume #8 level 0.009922
> volume #8 level 0.01085
> show #7 models
> hide #!8 models
> hide #9 models
> show #!6 models
> volume #6 level 0.00901
> hide #7 models
> hide #!6 models
> show #9 models
> show #!8 models
> volume #8 level 0.009392
> volume #8 level 0.01005
> volume #8 level 0.01019
> show #1 models
> show #!2 models
> hide #!8 models
> hide #9 models
> volume #2 level 0.01432
> hide #1 models
> show #3 models
> volume #2 level 0.01464
> volume #2 region 0,0,10,287,287,287
> hide #3 models
> hide #!2 models
> show #3 models
> show #!2 models
> show #1 models
> hide #1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> show #5 models
> show #!8 models
> hide #!8 models
> show #7 models
> hide #7 models
> hide #5 models
> hide #!2 models
> show #!2 models
> hide #3 models
> show #3 models
> hide #!2 models
> hide #3 models
> show #!4 models
> hide #!4 models
> show #!8 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> hide #!8 models
> show #5 models
> show #!4 models
> hide #!4 models
> hide #5 models
> show #9 models
> show #!8 models
> hide #!8 models
> hide #9 models
> show #!6 models
> show #7 models
> hide #7 models
> show #7 models
> hide #!6 models
> show #!6 models
> volume #2 level 0.01626
> volume #2 level 0.01497
> hide #!2 models
> volume #6 level 0.01132
> hide #!6 models
> hide #7 models
> show #9 models
> show #!8 models
> hide #!8 models
> ui tool show "Color Actions"
> hide #9 models
> show #9 models
> select add #9
1356 atoms, 1374 bonds, 186 residues, 1 model selected
> ui tool show "Color Actions"
> color sel slate blue target acs
> show #1 models
> hide #1 models
> color sel purple target acs
> color sel orchid target acs
> color sel medium orchid target acs
> show #1 models
> hide #1 models
> show #7 models
> hide #7 models
> color sel magenta target acs
> color sel hot pink target acs
> color sel blue violet target acs
> color sel medium orchid target acs
> color sel orchid target acs
> color sel medium orchid target acs
> color sel medium violet red target acs
> color sel medium orchid target acs
> color sel indigo target acs
> color sel medium slate blue target acs
> color sel slate blue target acs
[Repeated 1 time(s)]
> show #1 models
> hide #1 models
> color sel dark slate blue target acs
> color sel rebecca purple target acs
> color sel dark violet target acs
> color sel hot pink target acs
> color sel blue violet target acs
> color sel medium orchid target acs
> select clear
> show #!8 models
> hide #!8 models
> show #7 models
> hide #7 models
> show #1 models
> hide #1 models
> select add #9
1356 atoms, 1374 bonds, 186 residues, 1 model selected
> color sel blue violet target acs
> color sel orchid target acs
> color sel medium orchid target acs
> color sel medium violet red target acs
> color sel medium orchid target acs
> color sel orchid target acs
> color sel dark magenta target acs
> color sel purple target acs
> color sel plum target acs
> color sel violet target acs
[Repeated 1 time(s)]
> color sel indigo target acs
> color sel deep sky blue target acs
> color sel orchid target acs
> color sel medium orchid target acs
> color sel medium violet red target acs
> color sel medium orchid target acs
> color sel dark orchid target acs
> color sel medium violet red target acs
> color sel medium purple target acs
> color sel byhetero target acs
> select clear
> show #7 models
> hide #7 models
> hide #9 models
> show #9 models
> show #!8 models
> hide #!8 models
> show #7 models
> hide #7 models
> show #1 models
> hide #1 models
> show #1 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #!2 models
> show #3 models
> hide #9 models
> hide #!2 models
> hide #1 models
> hide #3 models
> show #1 models
> hide #1 models
> show #!2 models
> show #3 models
> hide #3 models
> show #1 models
> close #1
> show #3 models
> show #9 models
> hide #!2 models
> select add #3
2982 atoms, 3006 bonds, 198 residues, 1 model selected
> hide #9 models
> color sel cornflower blue target acs
> color sel byhetero target acs
> select clear
> hide #3 models
> show #7 models
> select add #7
1356 atoms, 1374 bonds, 186 residues, 1 model selected
> color sel dark sea green target acs
> color sel light green target acs
> color sel dark green target acs
> color sel green target acs
> color sel lime green target acs
> color sel spring green target acs
> color sel lawn green target acs
> color sel chartreuse target acs
> color sel forest green target acs
> color sel medium sea green target acs
> color sel sea green target acs
> color sel olive drab target acs
> color sel byhetero target acs
> color sel yellow green target acs
> color sel byhetero target acs
> color sel olive drab target acs
> color sel sea green target acs
> color sel byhetero target acs
> color sel dark olive green target acs
> color sel yellow green target acs
> color sel dark khaki target acs
> color sel olive target acs
> color sel lime target acs
> color sel green target acs
> color sel chartreuse target acs
> color sel lawn green target acs
> color sel spring green target acs
> color sel lime green target acs
> color sel forest green target acs
> color sel medium sea green target acs
> color sel teal target acs
> color sel medium spring green target acs
> color sel olive drab target acs
> color sel green yellow target acs
> color sel green target acs
[Repeated 3 time(s)]
> color sel lime target acs
> color sel chartreuse target acs
> color sel lawn green target acs
> color sel spring green target acs
> color sel lime green target acs
> color sel forest green target acs
> color sel medium sea green target acs
> color sel sea green target acs
> color sel medium sea green target acs
> color sel byhetero target acs
> select clear
> show #3 models
> hide #3 models
> show #9 models
> hide #9 models
> color #7 #00aa00ff
> select add #7
1356 atoms, 1374 bonds, 186 residues, 1 model selected
> color sel byhetero target acs
> select clear
> show #3 models
> hide #3 models
> show #9 models
> hide #9 models
> select add #7
1356 atoms, 1374 bonds, 186 residues, 1 model selected
> color sel green target acs
> color sel byhetero target acs
> select clear
> show #9 models
> hide #9 models
> select add #7
1356 atoms, 1374 bonds, 186 residues, 1 model selected
> color sel forest green target acs
> color sel byhetero target acs
> select clear
> show #9 models
> hide #9 models
> show #3 models
> hide #3 models
> show #!8 models
> hide #!8 models
> show #!6 models
> hide #!6 models
> select add #7
1356 atoms, 1374 bonds, 186 residues, 1 model selected
> color sel lime green target acs
> color sel medium sea green target acs
> color sel sea green target acs
> color #7 #00aa7fff
> color #7 #55aa00ff
> color #7 #55ff00ff
> color #7 springgreen
> color #7 lime
> color #7 #55aa00ff
> color #7 #55aa7fff
> color #7 #55aa00ff
> color #7 #00aa7fff
> color #7 #00aa00ff
> color #7 #265c4aff
> color #7 #28543eff
> color #7 #ccccccff
> color #7 #00aaffff
> color #7 #00aa7fff
> color #7 #00aa00ff
> color sel byhetero target acs
> select clear
> show #!8 models
> hide #!8 models
> show #!6 models
> hide #!6 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> close #4
> show #5 models
> hide #5 models
> close #5
> show #3 models
> hide #3 models
> show #!2 models
> show #3 models
> hide #3 models
> show #!8 models
> show #9 models
> hide #9 models
> show #9 models
> hide #!8 models
> hide #9 models
> hide #!2 models
> hide #7 models
> show #!2 models
> save "D:/YYX/data/Mice_amyloid/Model/Mouse model.cxs" includeMaps true
> show #3 models
> show #!6 models
> hide #!6 models
> show #7 models
> hide #7 models
> show #!8 models
> show #9 models
> hide #!8 models
> hide #9 models
> hide #3 models
> hide #!2 models
> show #!2 models
> show #3 models
> hide #3 models
> hide #!2 models
> show #!6 models
> hide #!6 models
> show #!8 models
> show #9 models
> hide #!8 models
> show #!8 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> hide #!8 models
> show #!8 models
> select add #8
2 models selected
> select subtract #8
Nothing selected
> select add #3
2982 atoms, 3006 bonds, 198 residues, 1 model selected
> select subtract #3
Nothing selected
> select add #2
2 models selected
> hide #!8 models
> show #!2 models
> hide #!2 models
> show #!2 models
> color sel cornflower blue target acs
> transparency #2.1 0
> select clear
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes true width 2
> select clear
> hide #!2 models
> show #!2 models
> show #!6 models
> hide #!2 models
> show #!2 models
> hide #!6 models
> volume #2 level 0.01685
> volume #!2 region all imageMode "full region"
> volume unzone #!2
> mousemode rightMode "crop volume"
> surface dust #2 size 8.3
> surface dust #2 size 0
[Repeated 1 time(s)]
> volume #2 level 0.01403
> volume #2 level 0.01308
> volume #2 level 0.0145
> volume #2 level 0.01544
> volume #2 level 0.0145
> volume #2 level 0.01434
> volume #2 level 0.014
> volume #2 level 0.0143
> volume #2 level 0.0142
> volume #2 level 0.014
> volume #2 level 0.0142
> show #3 models
> hide #3 models
> save D:/YYX/WorkReport/202412/5FAD_6M_Type3.png width 1341 height 820
> supersample 3 transparentBackground true
> save D:/YYX/WorkReport/202412/5FAD_6M_Type3_top.png width 1341 height 820
> supersample 3 transparentBackground true
> color #2 white models
> select add #2
2 models selected
> transparency #2.1 80
> select clear
> show #3 models
> volume zone #2 nearAtoms #3 range 4.98
> volume zone #2 nearAtoms #3 range 2
> volume #2 level 0.02047
> volume #2 level 0.01922
> volume #!2 region all imageMode "full region"
> volume unzone #!2
> mousemode rightMode "crop volume"
> volume #2 level 0.01436
> volume #2 level 0.01608
> volume #2 level 0.0142
> volume #2 level 0.02063
> volume #2 level 0.142
> volume #2 level 0.0142
> combine #3
> hide #!2 models
> hide #3 models
> hide #1 models
> show #1 models
> rename #1 "copy of Type3_1layer_R2.pdb"
> select add #1/D:28@CE
1 atom, 4 bonds, 1 residue, 1 model selected
> select up
8 atoms, 4 bonds, 4 residues, 1 model selected
> select up
52 atoms, 48 bonds, 4 residues, 1 model selected
> select up
152 atoms, 148 bonds, 12 residues, 1 model selected
> select up
1988 atoms, 2004 bonds, 132 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!2 models
> select clear
> volume zone #2 nearAtoms #1 range 4.98
> volume zone #2 nearAtoms #1 range 2
> volume #2 level 0.01922
> volume #2 level 0.0142
> hide #1 models
> show #1 models
> hide #!2 models
> show #!2 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> select add #1
994 atoms, 1002 bonds, 66 residues, 1 model selected
> volume #!2 region all imageMode "full region"
> volume unzone #!2
> mousemode rightMode "crop volume"
> select clear
> select add #2
2 models selected
> ui tool show "Segment Map"
Segmenting 5fad_Type3, density threshold 0.014200
Showing 44 region surfaces
392 watershed regions, grouped to 44 regions
Showing 5fad_Type3.seg - 44 regions, 44 surfaces
> select #4.42
1 model selected
> select add #4.29
2 models selected
Grouped 2 regions
> select add #4.41
2 models selected
> select add #4.30
3 models selected
> select subtract #4.29
2 models selected
> select add #4.29
3 models selected
Grouped 3 regions
Grouped 40 regions
> select clear
> select #4.29
1 model selected
> select #4.1
1 model selected
Opened 5fad_Type3_imasked as #5, grid size 288,288,288, pixel 0.83, shown at
step 1, values float32
> hide #!4 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!5 models
> show #!5 models
> rename #5 5fad_Type3_ED
> show #!2 models
> select add #2
3 models selected
Volume zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 2 maps.
> hide #!5 models
> select add #1
994 atoms, 1002 bonds, 66 residues, 4 models selected
> select subtract #1
3 models selected
> select add #1
994 atoms, 1002 bonds, 66 residues, 4 models selected
> select add #4
994 atoms, 1002 bonds, 66 residues, 6 models selected
> select subtract #4
994 atoms, 1002 bonds, 66 residues, 3 models selected
> hide #1 models
> show #1 models
> hide #!2 models
> show #!2 models
> volume zone #2 nearAtoms sel & #1 range 4.98
> volume zone #2 nearAtoms sel & #1 range 2
> select clear
> show #!5 models
> select clear
> save "D:/YYX/WorkReport/202412/5FAD_6M_Type3_model in map.png" width 1318
> height 820 supersample 3 transparentBackground true
> hide #1 models
> hide #!2 models
> hide #!5 models
> show #9 models
> show #!8 models
> volume #8 level 0.01121
> volume #8 level 0.01159
> volume #8 level 0.01337
> volume #8 level 0.01273
> volume #8 level 0.01082
> select add #8
2 models selected
> surface dust #8 size 8.3
> surface dust #8 size 3
> surface dust #8 size 2
> surface dust #8 size 0
> surface dust #8 size 1
> surface dust #8 size 2
> surface dust #8 size 2.5
> surface dust #8 size 2
> volume #8 level 0.009679
> volume #8 region 0,0,26,287,287,287
> surface dust #8 size 0
> select #8
2 models selected
> select clear
> volume #8 level 0.01
> volume #8 level 0.015
> volume #8 level 0.013
> volume #8 level 0.01084
> volume #8 level 0.011
> select add #9
1356 atoms, 1374 bonds, 186 residues, 1 model selected
> select add #8
1356 atoms, 1374 bonds, 186 residues, 3 models selected
> select subtract #8
1356 atoms, 1374 bonds, 186 residues, 1 model selected
> volume zone #8 nearAtoms sel & #9 range 4.98
> volume zone #8 nearAtoms sel & #9 range 2
> volume #!8 region all imageMode "full region"
> volume unzone #!8
> mousemode rightMode "crop volume"
> select clear
> combine #9
> rename #10 "copy of 5FAD_Type2_1layer_C1_R2_real_space_refined.pdb"
> hide #9 models
> hide #!8 models
> select #10/D:41@CA
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 3 bonds, 5 residues, 1 model selected
> select up
32 atoms, 28 bonds, 5 residues, 1 model selected
> select up
75 atoms, 71 bonds, 11 residues, 1 model selected
> select up
904 atoms, 916 bonds, 124 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select clear
Drag select of 7 atoms, 7 bonds
> select clear
> show #!8 models
> volume zone #8 nearAtoms #10 range 4.98
> volume zone #8 nearAtoms #10 range 2
> select clear
> save "D:/YYX/WorkReport/202412/5FAD_6M_Type2_model in map.png" width 1318
> height 820 supersample 3 transparentBackground true
> hide #!8 models
> show #!8 models
> show #9 models
> hide #10 models
> show #10 models
> hide #!8 models
> hide #9 models
> show #!8 models
> show #9 models
> hide #9 models
> hide #10 models
> volume #!8 region all imageMode "full region"
> volume unzone #!8
> mousemode rightMode "crop volume"
> select add #8
2 models selected
> color sel medium purple target acs
> select clear
> transparency #8 0
> select clear
> save D:/YYX/WorkReport/202412/5FAD_6M_Type2_top.png width 1318 height 820
> supersample 3 transparentBackground true
> save D:/YYX/WorkReport/202412/5FAD_6M_Type2.png width 1318 height 820
> supersample 3 transparentBackground true
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!6 models
> show #7 models
> combine #7
> rename #11 "copy of ApoE4_Type2_1layer_R1_real_space_refined.pdb"
> hide #7 models
> hide #!6 models
> select add #11/C:28@NZ
1 atom, 2 bonds, 1 residue, 1 model selected
> select add #11/E:28@CD
2 atoms, 2 bonds, 2 residues, 1 model selected
> select up
6 atoms, 2 bonds, 4 residues, 1 model selected
> select up
33 atoms, 29 bonds, 4 residues, 1 model selected
> select up
45 atoms, 41 bonds, 7 residues, 1 model selected
> select up
904 atoms, 916 bonds, 124 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select clear
> show #!6 models
> volume #6 level 0.009351
> volume #6 level 0.009474
> select add #11
452 atoms, 458 bonds, 62 residues, 1 model selected
> volume zone #6 nearAtoms sel & #11 range 4.98
> volume zone #6 nearAtoms sel & #11 range 2
> select clear
> volume #6 level 0.01058
> show #!5 models
> hide #!5 models
> volume #!6 region all imageMode "full region"
> volume unzone #!6
> mousemode rightMode "crop volume"
> volume #6 level 0.009597
> volume #6 level 0.01
> volume #6 level 0.008
> volume #6 level 0.009
> volume #6 level 0.0095
> volume #6 level 0.009
> volume #6 level 0.0092
> volume zone #6 nearAtoms #11 range 4.98
> volume zone #6 nearAtoms #11 range 2
> volume #6 region 0,0,0,287,287,287
> volume #6 level 0.0095
> volume #!6 region all imageMode "full region"
> volume unzone #!6
> mousemode rightMode "crop volume"
> volume zone #6 nearAtoms #11 range 4.98
> volume zone #6 nearAtoms #11 range 2
> volume #6 level 0.01184
> volume #6 level 0.0095
> volume #6 level 0.00987
> volume #!6 region all imageMode "full region"
> volume unzone #!6
> mousemode rightMode "crop volume"
> volume #6 level 0.01
> volume #6 level 0.098
> volume #6 level 0.0098
> volume #6 level 0.0095
> volume #6 level 0.0098
> volume zone #6 nearAtoms #11 range 4.98
> volume zone #6 nearAtoms #11 range 2
> save D:/YYX/WorkReport/202412/ApoE4_5FAD_Type2.png width 1318 height 820
> supersample 3 transparentBackground true
> hide #!6 models
> hide #11 models
> show #11 models
> show #!8 models
> hide #!8 models
> show #1 models
> hide #1 models
> show #3 models
> hide #3 models
> show #9 models
> hide #9 models
> show #10 models
> hide #11 models
> show #9 models
> hide #9 models
> show #!8 models
> hide #!8 models
> show #9 models
> hide #9 models
> show #!8 models
> color #8 white models
> transparency #8,10 80
> hide #!8 models
> show #!8 models
> volume zone #8 nearAtoms #10 range 4.98
> volume zone #8 nearAtoms #10 range 2
> volume #!8 region all imageMode "full region"
> volume unzone #!8
> mousemode rightMode "crop volume"
> hide #!8 models
> hide #10 models
> show #11 models
> hide #11 models
> show #1 models
> show #!2 models
> show #3 models
> hide #1 models
> hide #!2 models
> show #!2 models
> hide #3 models
> show #1 models
> hide #1 models
> hide #!2 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #11 models
> hide #11 models
> show #7 models
> show #!6 models
> volume #!6 region all imageMode "full region"
> volume unzone #!6
> mousemode rightMode "crop volume"
> hide #7 models
> show #11 models
> volume #6 region 0,0,0,287,287,287
[Repeated 1 time(s)]
> hide #!6 models
> hide #11 models
> show #3 models
> hide #3 models
> show #!5 models
> hide #!5 models
> show #7 models
> hide #7 models
> show #!8 models
> show #9 models
> volume #8 region 0,0,0,286,287,287
> volume #8 region 0,0,0,285,287,287
> volume #8 region 0,0,0,284,287,287
[Repeated 2 time(s)]
> hide #!8 models
> hide #9 models
> show #11 models
> show #7 models
> hide #7 models
> show #!8 models
> hide #!8 models
> show #!6 models
> hide #11 models
> color #6 #00aa0033 models
> transparency #6 0
> volume #6 level 0.01264
> volume #6 level 0.012
> volume #6 level 0.01225
> volume #6 level 0.01
> volume #6 level 0.011
> volume #6 level 0.012
> volume #6 level 0.01286
> volume #6 level 0.012
> save D:/YYX/WorkReport/202412/ApoE4_5FAD_Type2_top.png width 1318 height 820
> supersample 3 transparentBackground true
> save D:/YYX/WorkReport/202412/ApoE4_5FAD_Type2_side.png width 1318 height
> 820 supersample 3 transparentBackground true
> color #6 #ffffff33 models
> transparency #6 80
> show #11 models
> volume zone #6 nearAtoms #11 range 4.98
> volume zone #6 nearAtoms #11 range 2
> save "D:/YYX/WorkReport/202412/ApoE4_5FAD_Type2_model in map.png" width 1318
> height 820 supersample 3 transparentBackground true
> hide #!6 models
> hide #11 models
> show #!2 models
> hide #!2 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!8 models
> open
> D:/YYX/data/Mice_amyloid/Model/5FAD_6M_Female/Type2/5FAD_Type2_3layer_C1_R6.pdb
Chain information for 5FAD_Type2_3layer_C1_R6.pdb #12
---
Chain | Description
A B C D E F | No description available
> style #12 stick
Changed 1356 atom styles
> show #10 models
> hide #12 models
> hide #10 models
> show #10 models
> close #10
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> close #9
> show #12 models
> hide #!8 models
> select add #12
1356 atoms, 1374 bonds, 186 residues, 1 model selected
> ui tool show "Color Actions"
> color sel medium purple target acs
> color sel byhetero target acs
> select clear
> combine #12
> hide #9 models
> hide #12 models
> show #12 models
> show #9 models
> hide #12 models
> hide #9 models
> show #9 models
> show #!8 models
> hide #!8 models
> select add #9/D:26@CA
1 atom, 2 bonds, 1 residue, 1 model selected
> select up
7 atoms, 3 bonds, 4 residues, 1 model selected
> select up
31 atoms, 27 bonds, 4 residues, 1 model selected
> select up
85 atoms, 81 bonds, 13 residues, 1 model selected
> select up
904 atoms, 916 bonds, 124 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!8 models
> show #12 models
> hide #12 models
> volume zone #8 nearAtoms #9 range 4.98
> volume zone #8 nearAtoms #9 range 2
> save "D:/YYX/WorkReport/202412/5FAD_6M_Type2_model in map.png" width 1318
> height 820 supersample 3 transparentBackground true
> hide #!8 models
> show #12 models
> hide #9 models
> show #9 models
> show #!8 models
> hide #9 models
> hide #!8 models
> open D:/YYX/data/Mice_amyloid/Model/7q4m.pdb
7q4m.pdb title:
Type II β-amyloid 42 filaments from human brain [more info...]
Chain information for 7q4m.pdb #10
---
Chain | Description | UniProt
A B C D E F G H I J | amyloid-β precursor protein | A4_HUMAN
Non-standard residues in 7q4m.pdb #10
---
UNX — unknown atom or ion
> select add #10
2270 atoms, 2290 bonds, 320 residues, 1 model selected
> style sel stick
Changed 2270 atom styles
> color sel gray
> color sel dark gray
> ui tool show "Color Actions"
> color sel byhetero target acs
> select clear
> hide #10 models
> show #10 models
> hide #12 models
> show #9 models
> hide #9 models
> show #12 models
> hide #10 models
> hide #12 models
> show #3 models
> hide #3 models
> show #10 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
226 atoms, 229 bonds, 31 residues, 1 model selected
> select clear
> hide #10 models
> show #!8 models
> hide #!8 models
> show #9 models
> hide #9 models
> show #12 models
> hide #12 models
> show #10 models
> hide #10 models
> show #12 models
> hide #12 models
> show #12 models
> hide #12 models
> show #9 models
> hide #9 models
> show #9 models
> select add #9
452 atoms, 458 bonds, 62 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> show sel surfaces
[Repeated 1 time(s)]
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> select clear
> show #12 models
> hide #!9 models
> show #12 cartoons
> hide #12 atoms
> hide #12 models
> show #!9 models
> hide #!9 models
> show #12 models
> show #10 models
> ui tool show Distances
> select #10/J:28@NZ
1 atom, 1 residue, 1 model selected
> select add #10/I:28@O
2 atoms, 2 residues, 1 model selected
> distance #10/J:28@NZ #10/I:28@O
Distance between 7q4m.pdb #10/J LYS 28 NZ and /I LYS 28 O: 3.126Å
> select #10/J:28@NZ
1 atom, 1 residue, 1 model selected
> select add #10/I:42@OXT
2 atoms, 2 residues, 1 model selected
> distance #10/J:28@NZ #10/I:42@OXT
Distance between 7q4m.pdb #10/J LYS 28 NZ and /I ALA 42 OXT: 3.439Å
> select #10/J:28@NZ
1 atom, 1 residue, 1 model selected
> select #10/G:42@OXT
1 atom, 1 residue, 1 model selected
> select add #10/J:28@NZ
2 atoms, 2 residues, 1 model selected
> distance #10/G:42@OXT #10/J:28@NZ
Distance between 7q4m.pdb #10/G ALA 42 OXT and /J LYS 28 NZ: 2.931Å
> select #10/J:28@NZ
1 atom, 1 residue, 1 model selected
> select add #10/G:28@O
2 atoms, 2 residues, 1 model selected
> distance #10/J:28@NZ #10/G:28@O
Distance between 7q4m.pdb #10/J LYS 28 NZ and /G LYS 28 O: 4.564Å
> select clear
> hide #12 models
> show #12 models
> hide #10 models
> hide #!13 models
> hide #13.1 models
> select add #12
1356 atoms, 1374 bonds, 186 residues, 1 model selected
> select subtract #12
Nothing selected
> select add #12
1356 atoms, 1374 bonds, 186 residues, 1 model selected
> style sel stick
Changed 1356 atom styles
> show sel atoms
> hide sel cartoons
> select clear
> select #12/A:28@NZ
1 atom, 1 residue, 1 model selected
> select add #12/E:28@O
2 atoms, 2 residues, 1 model selected
> distance #12/A:28@NZ #12/E:28@O
Distance between 5FAD_Type2_3layer_C1_R6.pdb #12/A LYS 28 NZ and /E LYS 28 O:
5.598Å
> distance #12/A:28@NZ #12/E:28@O
Distance already exists; modify distance properties with 'distance style'
> select clear
[Repeated 1 time(s)]
> select #12/A:28@NZ
1 atom, 1 residue, 1 model selected
> select add #12/E:28@O
2 atoms, 2 residues, 1 model selected
> distance #12/A:28@NZ #12/E:28@O
Distance already exists; modify distance properties with 'distance style'
> show #!13 models
> show #13.1 models
> select #12/A:28@NZ
1 atom, 1 residue, 1 model selected
> select #12/D:28@O
1 atom, 1 residue, 1 model selected
> select add #12/A:28@NZ
2 atoms, 2 residues, 1 model selected
> distance #12/D:28@O #12/A:28@NZ
Distance between 5FAD_Type2_3layer_C1_R6.pdb #12/D LYS 28 O and /A LYS 28 NZ:
3.306Å
> select #12/A:28@NZ
1 atom, 1 residue, 1 model selected
> select add #12/D:42@OXT
2 atoms, 2 residues, 1 model selected
> distance #12/A:28@NZ #12/D:42@OXT
Distance between 5FAD_Type2_3layer_C1_R6.pdb #12/A LYS 28 NZ and /D ALA 42
OXT: 3.997Å
> hide #12 models
> show #10 models
> hide #10 models
> show #!9 models
> hide #!9 models
> show #12 models
> select #12/A:28@NZ
1 atom, 1 residue, 1 model selected
> select add #12/E:42@OXT
2 atoms, 2 residues, 1 model selected
> distance #12/A:28@NZ #12/E:42@OXT
Distance between 5FAD_Type2_3layer_C1_R6.pdb #12/A LYS 28 NZ and /E ALA 42
OXT: 7.688Å
> select clear
> show #!8 models
> hide #!8 models
> show #!8 models
> select add #8
2 models selected
> volume sel region all imageMode "full region"
> volume unzone sel
> mousemode rightMode "crop volume"
> select clear
> ~distance #10/J:28@NZ #10/I:28@O
> ~distance #12/A:28@NZ #12/E:42@OXT
> ~distance #10/G:42@OXT #10/J:28@NZ
> ~distance #12/A:28@NZ #12/D:42@OXT
> ~distance #12/A:28@NZ #12/E:28@O
> ~distance #10/J:28@NZ #10/I:42@OXT
> ~distance #12/D:28@O #12/A:28@NZ
> ~distance #10/J:28@NZ #10/G:28@O
> hide #!8 models
> hide #12 cartoons
> hide #12 atoms
> show #12 cartoons
> style #12 stick
Changed 1356 atom styles
> select add #12
1356 atoms, 1374 bonds, 186 residues, 1 model selected
> style sel stick
Changed 1356 atom styles
> hide sel cartoons
> show sel atoms
> select clear
> select #12/F:28@NZ
1 atom, 1 residue, 1 model selected
> select clear
> show #!8 models
> volume #8 level 0.003876
> hide #!2 models
> volume #6 level 0.011
> volume #8 level 0.011
> hide #!8 models
> show #7 models
> hide #12 models
> show #!6 models
> hide #7 models
> show #!8 models
> show #!9 models
> hide #!6 models
> hide #!9 models
> show #12 models
> volume #8 region 0,0,10,287,287,287
> volume #8 region 0,0,14,287,287,287
> save "D:/YYX/data/Mice_amyloid/Model/Mouse model.cxs" includeMaps true
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 299, in process
return copy_state(data, convert=convert)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 219, in copy_state
return _copy(data)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 207, in _copy
return data.copy()
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 91.1 MiB for an
array with shape (288, 288, 288) and data type uint32
During handling of the above exception, another exception occurred:
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 625, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000001D9A2B68B50> ->
<chimerax.segger.segment_dialog.VolumeSegmentationDialog object at
0x000001D9B747C070> 'segment map' -> <chimerax.segger.regions.Segmentation
object at 0x000001D9B1CE9A30> '5fad_Type3.seg': Unable to allocate 91.1 MiB
for an array with shape (288, 288, 288) and data type uint32
ValueError: error processing: 'tools' -> -> 'segment map' -> '5fad_Type3.seg':
Unable to allocate 91.1 MiB for an array with shape (288, 288, 288) and data
type uint32
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 299, in process
return copy_state(data, convert=convert)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 219, in copy_state
return _copy(data)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 207, in _copy
return data.copy()
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 91.1 MiB for an
array with shape (288, 288, 288) and data type uint32
During handling of the above exception, another exception occurred:
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 625, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000001D9A2B68B50> ->
<chimerax.segger.segment_dialog.VolumeSegmentationDialog object at
0x000001D9B747C070> 'segment map' -> <chimerax.segger.regions.Segmentation
object at 0x000001D9B1CE9A30> '5fad_Type3.seg': Unable to allocate 91.1 MiB
for an array with shape (288, 288, 288) and data type uint32
ValueError: error processing: 'tools' -> -> 'segment map' -> '5fad_Type3.seg':
Unable to allocate 91.1 MiB for an array with shape (288, 288, 288) and data
type uint32
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 475.14
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 (2)
comment:1 by , 8 months ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → ArrayMemoryError saving session with maps |
comment:2 by , 8 months ago
| Resolution: | → limitation |
|---|---|
| Status: | assigned → closed |
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They got an out of memory error trying to allocate a 90 Mbyte numpy array for saving a session that includes maps. It doesn't look like they had much data open and the machine has 16 Gbytes of memory. These out of memory errors are always on Windows but I can't explain them. Earlier in the session the user got an error message of no disk space left when ChimeraX tried to save the file history.
OSError: [Errno 28] No space left on device
Maybe this is related to the out-of-memory problem.