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Opened 5 months ago
Last modified 5 months ago
#17984 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-10-10.0.26100
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open C:/Users/mirai/OneDrive/ドキュメント/研究室/論文作成/P-CTD複合体/Fig/Fig-2-01.cxs
Opened dimer-J777_006_volume_map_sharp.mrc as #1, grid size 540,540,540, pixel
0.993, shown at level 0.18, step 1, values float32
Opened dimer-J777_006_volume_map_sharp.mrc as #3, grid size 540,540,540, pixel
0.993, shown at level 0.141, step 1, values float32
Opened tetramer-J741_003_volume_map_sharp.mrc as #4, grid size 540,540,540,
pixel 0.993, shown at level 0.0743, step 1, values float32
Log from Thu May 1 20:38:57 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open C:/Users/mirai/OneDrive/ドキュメント/研究室/論文作成/P-CTD複合体/Fig/Fig-1-02.cxs
Opened dimer-J777_006_volume_map_sharp.mrc as #1, grid size 540,540,540, pixel
0.993, shown at level 0.18, step 1, values float32
Opened dimer-J777_006_volume_map_sharp.mrc as #3, grid size 540,540,540, pixel
0.993, shown at level 0.141, step 1, values float32
Opened tetramer-J741_003_volume_map_sharp.mrc as #4, grid size 540,540,540,
pixel 0.993, shown at level 0.0681, step 1, values float32
Log from Tue Apr 22 18:07:24 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> set bgColor #ffffff00
Log from Wed Mar 19 15:09:37 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open C:/Users/mirai/OneDrive/ドキュメント/研究室/研究について/pYSTAT1/RVP-
> pYSTAT１複合体構造解析/250207_最新版/dimer-J777_006_volume_map_sharp.mrc
Opened dimer-J777_006_volume_map_sharp.mrc as #1, grid size 540,540,540, pixel
0.993, shown at level 0.0299, step 4, values float32
> volume #1 level 0.09491
> volume #1 step 1
> ui tool show "Color Actions"
> set bgColor white
[Repeated 1 time(s)]
> volume #1 level 0.1161
> volume #1 level 0.1409
> open C:/Users/mirai/OneDrive/ドキュメント/研究室/研究について/pYSTAT1/RVP-
> pYSTAT１複合体構造解析/250207_最新版/dimer-J759-FitJ520-NTD-
> dimer-2_real_space_refined_032-coot-4.pdb
Chain information for dimer-J759-FitJ520-NTD-
dimer-2_real_space_refined_032-coot-4.pdb #2
---
Chain | Description
A | No description available
B C | No description available
D | No description available
E | No description available
11 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> ui tool show "Model Panel"
> hide atoms
> show cartoons
> volume style surface
> transparency 50
> hide #!1 models
> select /A
861 atoms, 875 bonds, 108 residues, 1 model selected
> color sel blue
> select /B
4504 atoms, 4600 bonds, 2 pseudobonds, 552 residues, 2 models selected
> color (#!2 & sel) forest green
> select /C
4504 atoms, 4600 bonds, 2 pseudobonds, 552 residues, 2 models selected
> color (#!2 & sel) lime
> select /D
1071 atoms, 1095 bonds, 125 residues, 1 model selected
> color sel purple
> select /E
1056 atoms, 1080 bonds, 122 residues, 1 model selected
> color sel hot pink
> select clear
> show #!1 models
> open C:/Users/mirai/OneDrive/ドキュメント/研究室/研究について/pYSTAT1/RVP-
> pYSTAT１複合体構造解析/250207_最新版/dimer-J777_006_volume_map_sharp.mrc
Opened dimer-J777_006_volume_map_sharp.mrc as #3, grid size 540,540,540, pixel
0.993, shown at level 0.0299, step 4, values float32
> volume #3 level 0.1261
> volume #3 step 1
> volume #3 level 0.141
> color zone #1 near #2 distance 5.96
> transparency #1.1 0
> hide #!1 models
> show #!1 models
> hide #!2 models
> surface dust #1 size 9.93
> save C:/Users/mirai/OneDrive/ドキュメント/研究室/論文作成/P-CTD複合体/Fig/Fig1-1.png width
> 701 height 521 supersample 3
> save C:/Users/mirai/OneDrive/ドキュメント/研究室/論文作成/P-CTD複合体/Fig/Fig1-2.png width
> 701 height 521 supersample 3
> open C:/Users/mirai/OneDrive/ドキュメント/研究室/研究について/pYSTAT1/RVP-
> pYSTAT１複合体構造解析/250207_最新版/tetramer-J741_003_volume_map_sharp.mrc
Opened tetramer-J741_003_volume_map_sharp.mrc as #4, grid size 540,540,540,
pixel 0.993, shown at level 0.012, step 4, values float32
> volume #4 level 0.08145
> volume #4 step 1
> open C:/Users/mirai/OneDrive/ドキュメント/研究室/研究について/pYSTAT1/RVP-
> pYSTAT１複合体構造解析/250207_最新版/J741-tetramer-2.pdb
Summary of feedback from opening
C:/Users/mirai/OneDrive/ドキュメント/研究室/研究について/pYSTAT1/RVP-
pYSTAT１複合体構造解析/250207_最新版/J741-tetramer-2.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
14315 messages similar to the above omitted
Chain information for J741-tetramer-2.pdb #5
---
Chain | Description
A D | No description available
B C E F | No description available
22 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #!5 atoms
> hide #!5 cartoons
> show #!5 cartoons
Computing secondary structure
> transparency #4.1 50
> hide #!4 models
> select #5/A
861 atoms, 875 bonds, 108 residues, 1 model selected
> color sel blue
> select #2/B
4504 atoms, 4600 bonds, 2 pseudobonds, 552 residues, 2 models selected
> select #5/B
4192 atoms, 4283 bonds, 3 pseudobonds, 548 residues, 2 models selected
> color (#!5 & sel) orange
> select #5/C
4192 atoms, 4283 bonds, 3 pseudobonds, 548 residues, 2 models selected
> color (#!5 & sel) cyan
> select #5/D
861 atoms, 875 bonds, 108 residues, 1 model selected
> color sel blue
> select #5/E
4192 atoms, 4283 bonds, 3 pseudobonds, 548 residues, 2 models selected
> color (#!5 & sel) lime
> select #5/F
4192 atoms, 4283 bonds, 3 pseudobonds, 548 residues, 2 models selected
> color (#!5 & sel) forest green
> select clear
> show #!4 models
> color #4 #00000080 models
> color #4 #3b3b3b80 models
> volume #4 level 0.07165
> volume #4 level 0.06097
> color zone #4 near #5 distance 5.96
> volume #4 color #bdbdbd80
> color zone #4 near #5 distance 5.96
> volume #4 level 0.06898
> volume #4 level 0.07967
> hide #!4 models
> show #!4 models
> hide #!5 models
> volume #4 level 0.08679
> volume #4 level 0.06364
> volume #4 level 0.05651
> save C:/Users/mirai/OneDrive/ドキュメント/研究室/論文作成/P-CTD複合体/Fig/Fig1-3.png width
> 701 height 521 supersample 3
> save C:/Users/mirai/OneDrive/ドキュメント/研究室/論文作成/P-CTD複合体/Fig/Fig1-4.png width
> 701 height 521 supersample 3
monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.
monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY2', defaulting
to 96 DPI.
monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.
monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY2', defaulting
to 96 DPI.
monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.
monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY2', defaulting
to 96 DPI.
monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.
monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY2', defaulting
to 96 DPI.
monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.
monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY2', defaulting
to 96 DPI.
> save C:/Users/mirai/OneDrive/ドキュメント/研究室/論文作成/P-CTD複合体/Fig/Fig-1.cxs
——— End of log from Wed Mar 19 15:09:37 2025 ———
opened ChimeraX session
> ui tool show "Model Panel"
> show #!2 models
> hide #!1 models
> select #2/D
1071 atoms, 1095 bonds, 125 residues, 1 model selected
> color sel cyan
> select #2/E
1056 atoms, 1080 bonds, 122 residues, 1 model selected
> color sel lime
> select clear
> show #!1 models
> color zone #1 near #2 distance 5.96
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> volume #4 level 0.06809
> volume #1 level 0.1939
> volume #1 level 0.18
> save C:/Users/mirai/OneDrive/ドキュメント/研究室/論文作成/P-CTD複合体/Fig/Fig-1-02.cxs
——— End of log from Tue Apr 22 18:07:24 2025 ———
opened ChimeraX session
> show #!2 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> show #!5 models
> show #!4 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> show #!4 models
> transparency #4.1 0
> transparency #4.1 50
> show #!2 models
> show #!3 models
> hide #!3 models
> show #!1 models
> hide #!1 models
> open C:/Users/mirai/OneDrive/ドキュメント/研究室/研究について/pYSTAT1/RVP-
> pYSTAT１複合体構造解析/250207_最新版/J741-tetramer-3.pdb
Summary of feedback from opening
C:/Users/mirai/OneDrive/ドキュメント/研究室/研究について/pYSTAT1/RVP-
pYSTAT１複合体構造解析/250207_最新版/J741-tetramer-3.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
16442 messages similar to the above omitted
Chain information for J741-tetramer-3.pdb #6
---
Chain | Description
A D | No description available
B C E F | No description available
G I | No description available
H J | No description available
22 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #!4 models
> hide atoms
> show cartoons
Computing secondary structure
> hide #!5 models
> hide #!2 models
> show #!4 models
> fitmap #6 inMap #4
Fit molecule J741-tetramer-3.pdb (#6) to map
tetramer-J741_003_volume_map_sharp.mrc (#4) using 22744 atoms
average map value = 0.09438, steps = 60
shifted from previous position = 0.0465
rotated from previous position = 0.0202 degrees
atoms outside contour = 8453, contour level = 0.068091
Position of J741-tetramer-3.pdb (#6) relative to
tetramer-J741_003_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.99999994 -0.00029561 -0.00016987 0.08526723
0.00029563 0.99999995 0.00009184 -0.08960324
0.00016985 -0.00009189 0.99999998 -0.04071487
Axis -0.26017627 -0.48104665 0.83719916
Axis point 324.56715241 276.79082142 0.00000000
Rotation angle (degrees) 0.02023141
Shift along axis -0.01316763
> hide #!4 models
> select #6/A
861 atoms, 875 bonds, 108 residues, 1 model selected
> color sel blue
> select #6/B
4192 atoms, 4283 bonds, 3 pseudobonds, 548 residues, 2 models selected
> color (#!6 & sel) orange
> select #6/C
4192 atoms, 4283 bonds, 3 pseudobonds, 548 residues, 2 models selected
> color (#!6 & sel) cyan
> select #6/D
861 atoms, 875 bonds, 108 residues, 1 model selected
> color sel blue
> select #6/E
4192 atoms, 4283 bonds, 3 pseudobonds, 548 residues, 2 models selected
> color (#!6 & sel) lime
> select #6/F
4192 atoms, 4283 bonds, 3 pseudobonds, 548 residues, 2 models selected
> color (#!6 & sel) forest green
> select #6/G
1071 atoms, 1095 bonds, 125 residues, 1 model selected
> color sel cyan
> select #6/H
1056 atoms, 1080 bonds, 122 residues, 1 model selected
> color sel lime
> select #6/I
1071 atoms, 1095 bonds, 125 residues, 1 model selected
> color sel forest green
> select #6/J
1056 atoms, 1080 bonds, 122 residues, 1 model selected
> color sel orange
> hide #!6 models
> show #!6 models
> select add #6
22744 atoms, 23232 bonds, 12 pseudobonds, 2902 residues, 2 models selected
> select subtract #6
Nothing selected
> show #!4 models
> color zone #4 near #6 distance 5.96
> transparency #4.1 0
> transparency #4.1 50
Drag select of 4 tetramer-J741_003_volume_map_sharp.mrc , 21 residues
> select add #6
22744 atoms, 23232 bonds, 12 pseudobonds, 2902 residues, 4 models selected
> volume #4 level 0.08768
> volume #4 level 0.07878
> volume #4 level 0.07165
> color zone #4 near sel & #6 distance 5.96
> transparency sel 0
> transparency sel 50
> select subtract #6
2 models selected
> select subtract #4
Nothing selected
> volume #4 level 0.05651
> volume #4 level 0.07433
> color zone #4 near #6 distance 5.96
> transparency #4.1 0
> transparency #4.1 50
> camera ortho
> set bgColor white
> lighting soft intensity 0.1
> lighting shadows false
> graphics silhouettes true width 1 depthJump 0.01
> save C:/Users/mirai/OneDrive/ドキュメント/研究室/論文作成/P-CTD複合体/Fig/Fig-2-01.cxs
——— End of log from Thu May 1 20:38:57 2025 ———
opened ChimeraX session
> transparency #4.1 0
> transparency #4.1 50
> select #6/G
1071 atoms, 1095 bonds, 125 residues, 1 model selected
> color sel purple
> select #6/A
861 atoms, 875 bonds, 108 residues, 1 model selected
> select #6/B
4192 atoms, 4283 bonds, 3 pseudobonds, 548 residues, 2 models selected
> select #6/C
4192 atoms, 4283 bonds, 3 pseudobonds, 548 residues, 2 models selected
> color (#!6 & sel) purple
> color zone #4 near sel & #6 distance 5.96
[Repeated 1 time(s)]
> select clear
> color zone #4 near #6 distance 5.96
> transparency #4.1 0
> transparency #4.1 50
> save C:\Users\mirai/Downloads/Fig1-35.png width 4000 height 4000
> transparentBackground true
> color zone #1 near #6 distance 5.96
> transparency #1.1 0
> ui tool show "Model Panel"
You can double click a model's Name or ID in the model panel to edit those
fields
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!6 models
> select #2/D
1071 atoms, 1095 bonds, 125 residues, 1 model selected
> color sel purple
> transparency #1.1 50
> select clear
> save C:\Users\mirai/Downloads/Fig1-36.png width 4000 height 4000
> transparentBackground true
> hide #!1 models
> hide #!2 models
> show #!6 models
> show #!4 models
> save C:\Users\mirai/Downloads/Fig1-37.png width 4000 height 4000
> transparentBackground true
> hide #!4 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!3 models
> show #!6 models
> color zone #3 near #6 distance 5.96
> hide #!6 models
> volume #4 level 0.06898
> volume #3 level 0.07738
> volume #3 level 0.2859
> volume #3 level 0.2294
> volume #3 level 0.1763
> volume #3 color black
> volume #3 color #9f9f9f
> show #!2 models
> color zone #3 near #2 distance 5.96
> hide #!2 models
> show #!5 models
> hide #!5 models
> show #!6 models
> color zone #3 near #6 distance 5.96
> hide #!6 models
> show #!6 models
> show #!5 models
> hide #!5 models
> show #!2 models
Color zone shortcut requires 1 displayed atomic model and 1 map, got 2 atomic
models, 1 maps.
[Repeated 1 time(s)]
> hide #!2 models
> hide #!3 models
> show #!3 models
> show #!2 models
> hide #!2 models
> hide #!6 models
> color #3 #005500ff models
> show #!5 models
> hide #!5 models
> show #!6 models
> color zone #3 near #6 distance 5.96
> hide #!3 models
> show #!3 models
> hide #!6 models
> surface dust #3 size 9.93
> volume #3 level 0.1622
> volume #3 level 0.141
> volume #3 level 0.1622
> save C:\Users\mirai/Downloads/Fig1-38.png width 4000 height 4000
> transparentBackground true
> volume #3 level 0.1375
> save C:\Users\mirai/Downloads/Fig1-39.png width 4000 height 4000
> transparentBackground true
> volume #3 level 0.1481
> volume #3 level 0.1622
> volume sharpen #1 bfactor -200
Opened dimer-J777_006_volume_map_sharp.mrc gaussian as #7, grid size
540,540,540, pixel 0.993, shown at step 1, values float32
> volume sharpen #1 bfactor -100
Opened dimer-J777_006_volume_map_sharp.mrc gaussian as #8, grid size
540,540,540, pixel 0.993, shown at step 1, values float32
> volume #7 level 0.1337
> volume #8 level 0.1749
> show #!6 models
> color zone #7 near #6 distance 5.96
> hide #!6 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> color #7 #55007fff models
> show #!3 models
> hide #!3 models
> show #!2 models
> color zone #7 near #2 distance 5.96
> hide #!2 models
> color #7 #6b00a1ff models
Color zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
models, 1 maps.
> show #!2 models
> color zone #7 near #2 distance 5.96
> color #7 #f3f3f3ff models
> color #7 white models
> show #!6 models
> color #7 #9f039fff models
> color #7 #590059ff models
> hide #!2 models
> show #!2 models
> hide #!6 models
> hide #!2 models
Color zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
models, 1 maps.
> show #!2 models
> color zone #7 near #2 distance 5.96
> show #!5 models
> hide #!5 models
> show #!6 models
> color #7 #4c004cff models
> color #7 #9a009aff models
> hide #!6 models
> color zone #7 near #2 distance 5.96
> hide #!2 models
> show #!3 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> hide #!3 models
> show #!7 models
> hide #!7 models
> show #!3 models
> hide #!3 models
> show #!7 models
> hide #!7 models
> show #!8 models
> color #8 #55007fff models
> show #!6 models
> color #8 white models
> color #8 #9e009eff models
> hide #!6 models
> show #!2 models
> color zone #8 near #2 distance 5.96
> hide #!2 models
> hide #!8 models
> show #!3 models
> hide #!3 models
> show #!8 models
> volume #8 level 0.1675
> volume #8 level 0.1601
> save C:\Users\mirai/Downloads/Fig1-41.png width 4000 height 4000
> transparentBackground true
> open
> C:/Users/mirai/OneDrive/ドキュメント/研究室/研究について/pYSTAT1/pYSTAT1-DNAの構造解析/pYSTAT1-DNAのモデリング方法_杉田先生へ/tetramer_refined_expanded.pdb
Chain information for tetramer_refined_expanded.pdb #9
---
Chain | Description
A D G J | No description available
B F I L | No description available
C E H K | No description available
> open
> C:/Users/mirai/OneDrive/ドキュメント/研究室/研究について/pYSTAT1/pYSTAT1-DNAの構造解析/pYSTAT1電顕マップ/tetramer/cryosparc_P35_cryosparc_P35_J178_005_volume_map_sharp_trimmed.mrc
Opened cryosparc_P35_cryosparc_P35_J178_005_volume_map_sharp_trimmed.mrc as
#10, grid size 122,122,122, pixel 1.76, shown at level 0.383, step 1, values
float32
> hide #!9 atoms
> show #!9 cartoons
Computing secondary structure
> hide #!9 models
> show #!9 models
> hide #!10 models
> select ::name="DA"::name="DC"::name="DG"::name="DT"
2952 atoms, 3304 bonds, 144 residues, 1 model selected
> color sel orange red
> select #9/A
4511 atoms, 4607 bonds, 2 pseudobonds, 553 residues, 2 models selected
> color (#!9 & sel) orange
> select #9/D
4511 atoms, 4607 bonds, 2 pseudobonds, 553 residues, 2 models selected
> color (#!9 & sel) purple
> select #9/G
4511 atoms, 4607 bonds, 2 pseudobonds, 553 residues, 2 models selected
> color (#!9 & sel) lime
> select #9/J
4511 atoms, 4607 bonds, 2 pseudobonds, 553 residues, 2 models selected
> color (#!9 & sel) forest green
> select clear
> show #!10 models
> color zone #10 near #9 distance 10.6
> transparency #10.1 50
> save C:\Users\mirai/Downloads/Fig1-42.png width 4000 height 4000
> transparentBackground true
[Repeated 1 time(s)]
> volume #10 level 0.2595
> color zone #10 near #9 distance 10.6
> transparency #10.1 50
> save C:\Users\mirai/Downloads/Fig1-43.png width 4000 height 4000
> transparentBackground true
> save C:/Users/mirai/OneDrive/ドキュメント/研究室/学会/2025_蛋白質科学会/口頭発表/Figure-1.cxs
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 1051, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 746, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\serialize.py", line 76, in msgpack_serialize
stream.write(packer.pack(obj))
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\safesave.py", line 148, in write
self._f.write(buf)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\lz4\frame\\__init__.py", line 740, in write
compressed = self._compressor.compress(data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\lz4\frame\\__init__.py", line 258, in compress
result = compress_chunk(
^^^^^^^^^^^^^^^
MemoryError
MemoryError
File "C:\Program Files\ChimeraX 1.9\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 1.9\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 127, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 1051, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 746, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\serialize.py", line 76, in msgpack_serialize
stream.write(packer.pack(obj))
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\safesave.py", line 148, in write
self._f.write(buf)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\lz4\frame\\__init__.py", line 740, in write
compressed = self._compressor.compress(data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\lz4\frame\\__init__.py", line 258, in compress
result = compress_chunk(
^^^^^^^^^^^^^^^
MemoryError
MemoryError
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\lz4\frame\\__init__.py", line 258, in compress
result = compress_chunk(
^^^^^^^^^^^^^^^
See log for complete Python traceback.
> save C:/Users/mirai/OneDrive/ドキュメント/研究室/学会/2025_蛋白質科学会/口頭発表/Figure_1.cxs
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 1051, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 746, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\serialize.py", line 76, in msgpack_serialize
stream.write(packer.pack(obj))
^^^^^^^^^^^^^^^^
File "msgpack\\\\_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack
File "msgpack\\\\_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack
File "msgpack\\\\_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack
File "msgpack\\\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
MemoryError
MemoryError
File "msgpack\\\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 127, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 1051, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\session.py", line 746, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\serialize.py", line 76, in msgpack_serialize
stream.write(packer.pack(obj))
^^^^^^^^^^^^^^^^
File "msgpack\\\\_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack
File "msgpack\\\\_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack
File "msgpack\\\\_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack
File "msgpack\\\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
MemoryError
MemoryError
File "msgpack\\\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
See log for complete Python traceback.
OpenGL version: 3.3.0 Core Profile Context 23.19.16.240618
OpenGL renderer: AMD Radeon (TM) Graphics
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.4
Locale: ja_JP.cp932
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows
Manufacturer: Dell Inc.
Model: Inspiron 14 7425 2-in-1
OS: Microsoft Windows 11 Home (Build 26100)
Memory: 7,893,946,368
MaxProcessMemory: 137,438,953,344
CPU: 12 AMD Ryzen 5 5625U with Radeon Graphics
OSLanguage: ja-JP
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2024.8.30
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.4.5
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pywin32: 306
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
WMI: 1.5.1
Change History (1)
comment:1 by , 5 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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Probably because of the maps produced by "volume sharpen"