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Opened 8 months ago
Closed 8 months ago
#16978 closed defect (limitation)
MemoryError saving maps in sessions
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | Greg Couch | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19045
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:
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/jlerath/Downloads/cryosparc_P49_J200_004_volume_map_sharp.mrc
> C:/Users/jlerath/Downloads/cryosparc_P49_J199_004_volume_map_sharp.mrc
> C:/Users/jlerath/Downloads/cryosparc_P49_J198_003_volume_map_sharp.mrc
Opened cryosparc_P49_J200_004_volume_map_sharp.mrc as #1.1, grid size
448,448,448, pixel 1.18, shown at level 0.124, step 2, values float32
Opened cryosparc_P49_J199_004_volume_map_sharp.mrc as #1.2, grid size
448,448,448, pixel 1.18, shown at level 0.132, step 2, values float32
Opened cryosparc_P49_J198_003_volume_map_sharp.mrc as #1.3, grid size
448,448,448, pixel 1.18, shown at level 0.204, step 2, values float32
> lighting soft
> set bgColor white
> surface dust #1 size 10
> volume #1 step 1
> volume #1 smoothSurfaces true
Expected a keyword
> volume #1 surfaceSmoothing true
> hide #!1 models
> open "C:/Users/jlerath/Desktop/Ec24
> CryoEM/J137/J198_003_volume_map_deepemhancer2.mrc"
Opened J198_003_volume_map_deepemhancer2.mrc as #2, grid size 448,448,448,
pixel 1.18, shown at level 0.0593, step 2, values float32
> open "C:/Users/jlerath/Desktop/Ec24
> CryoEM/J137/J199_004_volume_map_deepemhancer2.mrc"
Opened J199_004_volume_map_deepemhancer2.mrc as #3, grid size 448,448,448,
pixel 1.18, shown at level 0.0178, step 2, values float32
> open "C:/Users/jlerath/Desktop/Ec24
> CryoEM/J137/J200_004_volume_map_deepemhancer2.mrc"
Opened J200_004_volume_map_deepemhancer2.mrc as #4, grid size 448,448,448,
pixel 1.18, shown at level 0.0275, step 2, values float32
> hide #!4 models
> hide #!3 models
> volume #2 level 0.25
> volume #3 level 0.25
> volume #4 level 0.25
> volume #2-4 step 1
> surface dust #2-4 size 10
> surface dust #2-4 size 15
> surface dust #2-4 size 10
> surface dust #2-4 size 15
> show #!3 models
> show #!4 models
> hide #!2 models
> volume #4 level 0.15
> volume #4 level 0.2
> volume #3 level 0.2
> volume #2 level 0.2
> show #!2 models
> surface dust #2-4 size 25
> surface dust #2-4 size 50
> hide #!2 models
> surface dust #2-4 size 60
> surface dust #2-4 size 50
> show #!2 models
> hide #!3 models
> hide #!4 models
> surface dust #2-4 size 25
> surface dust #2-4 size 75
> surface dust #2-4 size 25
> surface dust #2-4 size 50
> surface dust #2-4 size 20
> surface dust #2-4 size 10
> surface dust #2-4 size 50
> show #!3 models
> hide #!2 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> show #!1 models
> hide #!1.3 models
> hide #!1.1 models
> show #!1.1 models
> hide #!3 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.1 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!1.1 models
> hide #!1 models
> show #!2 models
> volume #2 level 0.25
> volume #2 level 0.2
> surface dust #2-4 size 20
> surface dust #2-4 size 25
> surface dust #2 size 75
> surface dust #2 size 50
> surface dust #2 size 25
> surface dust #2 size 50
> surface dust #2 size 25
> surface dust #2 size 30
> surface dust #2 size 40
> surface dust #2 size 35
> surface dust #2 size 32
> surface dust #2 size 40
> volume mask #2 surfaces #2 fullMap true pad 0.25 extend 1
Opened J198_003_volume_map_deepemhancer2.mrc masked as #5, grid size
448,448,448, pixel 1.18, shown at step 1, values float32
> volume #5 level 0.05393
> volume #5 level 0.15
> volume #5 level 0.2
> surface dust #5 size 11.8
> save "C:/Users/jlerath/Desktop/Ec24
> CryoEM/J137/J198_003_volume_map_deepemhancer2_nodust.mrc" models #5
> hide #!5 models
> show #!3 models
> surface dust #3 size 25
> surface dust #3 size 10
> surface dust #3 size 15
> surface dust #3 size 20
> surface dust #3 size 15
> surface dust #3 size 10
> surface dust #3 size 15
> ui mousemode right "map eraser"
> volume erase #3 center 140.96,240.44,197.87 radius 32.946
Opened J199_004_volume_map_deepemhancer2.mrc copy as #7, grid size
448,448,448, pixel 1.18, shown at step 1, values float32
> surface dust #3 size 15
[Repeated 1 time(s)]
> surface dust 73 size 15
Missing or invalid "surfaces" argument: invalid surfaces specifier
> surface dust #7 size 15
> volume mask #7 surfaces #7 fullMap true pad 0.25 extend 1
Opened J199_004_volume_map_deepemhancer2.mrc copy masked as #6, grid size
448,448,448, pixel 1.18, shown at step 1, values float32
> volume #6 level 0.1232
> volume #6 level 0.2
No map chosen to save
> save "C:/Users/jlerath/Desktop/Ec24
> CryoEM/J137/J199_004_volume_map_deepemhancer2_nodust.mrc" models #6
> close #7
> hide #!6 models
> show #!4 models
> surface dust #4 size 15
> surface dust #4 size 20
> surface dust #4 size 25
> surface dust #4 size 30
> surface dust #4 size 50
> surface dust #4 size 75
> surface dust #4 size 100
> surface dust #4 size 50
> surface dust #4 size 45
> surface dust #4 size 50
> volume mask #4 surfaces #4 fullMap true pad 0.25 extend 1
Opened J200_004_volume_map_deepemhancer2.mrc masked as #7, grid size
448,448,448, pixel 1.18, shown at step 1, values float32
> save "C:/Users/jlerath/Desktop/Ec24
> CryoEM/J137/J200_004_volume_map_deepemhancer2_nodust.mrc" models #7
> open "C:/Users/jlerath/Desktop/Ec24
> CryoEM/J133/J187_004_volume_map_APEdeepemhancer2_tightmask_20250225.mrc"
Opened J187_004_volume_map_APEdeepemhancer2_tightmask_20250225.mrc as #8, grid
size 89,72,86, pixel 1.18,1.18,1.18, shown at level 0.68, step 1, values
float32
> volume #8 level 0.2084
> open "C:/Users/jlerath/Desktop/Ec24
> CryoEM/Masks/Ec24APEMask_J178_20250225.mrc"
Opened Ec24APEMask_J178_20250225.mrc as #9, grid size 448,448,448, pixel 1.18,
shown at level 5.95e-05, step 2, values float32
> hide #!8 models
> ui tool show "Fit in Map"
> close #8
> fitmap #9 inMap #7
Fit map Ec24APEMask_J178_20250225.mrc in map
J200_004_volume_map_deepemhancer2_nodust.mrc using 9131 points
correlation = 0.5413, correlation about mean = 0.4168, overlap = 476.3
steps = 108, shift = 1.47, angle = 1.11 degrees
Position of Ec24APEMask_J178_20250225.mrc (#9) relative to
J200_004_volume_map_deepemhancer2_nodust.mrc (#7) coordinates:
Matrix rotation and translation
0.99981435 -0.01892054 0.00364528 3.88172196
0.01892373 0.99982058 -0.00084170 -5.69111072
-0.00362870 0.00091053 0.99999300 1.79076680
Axis 0.04542191 0.18855830 0.98101102
Axis point 311.20491879 200.04097657 0.00000000
Rotation angle (degrees) 1.10521261
Shift along axis 0.85997106
> fitmap #9 inMap #7
Fit map Ec24APEMask_J178_20250225.mrc in map
J200_004_volume_map_deepemhancer2_nodust.mrc using 9131 points
correlation = 0.5414, correlation about mean = 0.4168, overlap = 476.2
steps = 156, shift = 0.00952, angle = 0.0179 degrees
Position of Ec24APEMask_J178_20250225.mrc (#9) relative to
J200_004_volume_map_deepemhancer2_nodust.mrc (#7) coordinates:
Matrix rotation and translation
0.99980934 -0.01920428 0.00353146 3.96743793
0.01920715 0.99981522 -0.00077957 -5.77542209
-0.00351584 0.00084725 0.99999346 1.77566756
Axis 0.04162087 0.18030047 0.98273061
Axis point 310.78665645 201.62289998 0.00000000
Rotation angle (degrees) 1.11981516
Shift along axis 0.86881977
> fitmap #9 inMap #7
Fit map Ec24APEMask_J178_20250225.mrc in map
J200_004_volume_map_deepemhancer2_nodust.mrc using 9131 points
correlation = 0.5416, correlation about mean = 0.4171, overlap = 476.3
steps = 68, shift = 0.0224, angle = 0.0343 degrees
Position of Ec24APEMask_J178_20250225.mrc (#9) relative to
J200_004_volume_map_deepemhancer2_nodust.mrc (#7) coordinates:
Matrix rotation and translation
0.99981985 -0.01870604 0.00321851 3.95310550
0.01870899 0.99982458 -0.00088878 -5.61651021
-0.00320132 0.00094884 0.99999443 1.67069055
Axis 0.04835036 0.16891532 0.98444393
Axis point 310.14525152 206.04784488 0.00000000
Rotation angle (degrees) 1.08886458
Shift along axis 0.88712060
> fitmap #9 inMap #7
Fit map Ec24APEMask_J178_20250225.mrc in map
J200_004_volume_map_deepemhancer2_nodust.mrc using 9131 points
correlation = 0.5415, correlation about mean = 0.417, overlap = 476.3
steps = 132, shift = 0.00747, angle = 0.0226 degrees
Position of Ec24APEMask_J178_20250225.mrc (#9) relative to
J200_004_volume_map_deepemhancer2_nodust.mrc (#7) coordinates:
Matrix rotation and translation
0.99981253 -0.01908992 0.00323694 4.03364088
0.01909259 0.99981740 -0.00079551 -5.73321232
-0.00322116 0.00085717 0.99999444 1.69559133
Axis 0.04263869 0.16661734 0.98509929
Axis point 309.99857685 206.27124589 0.00000000
Rotation angle (degrees) 1.11046375
Shift along axis 0.88706241
> fitmap #9 inMap #7
Fit map Ec24APEMask_J178_20250225.mrc in map
J200_004_volume_map_deepemhancer2_nodust.mrc using 9131 points
correlation = 0.5414, correlation about mean = 0.4168, overlap = 476.3
steps = 76, shift = 0.0187, angle = 0.027 degrees
Position of Ec24APEMask_J178_20250225.mrc (#9) relative to
J200_004_volume_map_deepemhancer2_nodust.mrc (#7) coordinates:
Matrix rotation and translation
0.99981659 -0.01880759 0.00361261 3.86319220
0.01881072 0.99982271 -0.00083408 -5.66445559
-0.00359628 0.00090188 0.99999313 1.78315472
Axis 0.04527545 0.18801472 0.98112211
Axis point 311.60664085 200.29850045 0.00000000
Rotation angle (degrees) 1.09848839
Shift along axis 0.85939928
> volume mask #9 surfaces #7 fullMap true pad 0.25 extend 1
Opened Ec24APEMask_J178_20250225.mrc masked as #8, grid size 448,448,448,
pixel 1.18, shown at step 1, values float32
> hide #!7 models
> ui tool show "Segment Map"
> close #9
Segmenting Ec24APEMask_J178_20250225.mrc masked, density threshold 0.000060
Showing 3 region surfaces
41 watershed regions, grouped to 3 regions
Showing Ec24APEMask_J178_20250225 masked.seg - 3 regions, 3 surfaces
> hide #!8 models
> ui mousemode right select
> select #9.2
1 model selected
> select #9.3
1 model selected
> select #9.1
1 model selected
Grouped 1 regions
Ungrouped to 1 regions
Ungrouped to 3 regions
> select #9.5
1 model selected
Ungrouped to 2 regions
> select #9.4
1 model selected
Ungrouped to 2 regions
> select #9.8
1 model selected
> select #9.5
1 model selected
> select #9.7
1 model selected
Drag select of 61, 30 of 13804 triangles, 57, 88 of 12984 triangles
> select #9.1
1 model selected
> select #9.1
1 model selected
> select add #9.6
2 models selected
Drag select of 57, 8 of 12984 triangles
> select add #9.5
4 models selected
Grouped 4 regions
> select clear
> select #9.1
1 model selected
> close #9
> show #!8 models
> volume gaussian #8 sDev 2
Opened Ec24APEMask_J178_20250225.mrc masked gaussian as #9, grid size
448,448,448, pixel 1.18, shown at step 1, values float32
Segmenting Ec24APEMask_J178_20250225.mrc masked gaussian, density threshold
0.000047
Showing 3 region surfaces
12 watershed regions, grouped to 3 regions
Showing Ec24APEMask_J178_20250225 masked gaussian.seg - 3 regions, 3 surfaces
> hide #!9 models
> select #10.2
1 model selected
> select #10.3
1 model selected
Ungrouped to 2 regions
> select #10.5
1 model selected
Ungrouped to 0 regions
> select #10.5
1 model selected
Ungrouped to 0 regions
> open "C:/Users/jlerath/Desktop/Ec24 CryoEM/7b5k-pdb-
> bundle2-Ec24Fitted_20250217.pdb"
Chain information for 7b5k-pdb-bundle2-Ec24Fitted_20250217.pdb #11
---
Chain | Description
6 | No description available
9 | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
n | No description available
o | No description available
p | No description available
q | No description available
r | No description available
s | No description available
t | No description available
u | No description available
v | No description available
x | No description available
z | No description available
> combine #11
> hide #11 models
> close #11
> select #12 /0
Nothing selected
> select #12 /9
2439 atoms, 2628 bonds, 76 residues, 1 model selected
> hide #!10 models
> select ~sel & ##selected
94119 atoms, 98393 bonds, 4443 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!10 models
> select #10.1
1 model selected
> select #10.4
1 model selected
> select add #10.5
2 models selected
> select #10.5
1 model selected
> select add #10.4
2 models selected
Saving 2 regions to mrc file...
Opened Ec24ESiteMask_J200_20250225.mrc as #11, grid size 34,32,39, pixel 1.18,
shown at step 1, values float32
Wrote Ec24ESiteMask_J200_20250225.mrc
> select #11
2 models selected
> close #11
> select #10.1
1 model selected
> select #10.1
1 model selected
Saving 1 regions to mrc file...
Opened Ec24ESiteMask_J200_20250225.mrc as #11, grid size 43,53,81, pixel 1.18,
shown at step 1, values float32
Wrote Ec24ESiteMask_J200_20250225.mrc
> hide #!10 models
> select clear
> volume #11 level 0.06184
> volume #11 level 0.006871
> transparency #11 50
> show #!10 models
> hide #!11 models
> show #!11 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> volume #11 level 1e-06
> volume #11 level 4.74e-05
> hide #!10 models
> ui tool show "Fit in Map"
> fitmap #12 inMap #11
Fit molecule copy of 7b5k-pdb-bundle2-Ec24Fitted_20250217.pdb (#12) to map
Ec24ESiteMask_J200_20250225.mrc (#11) using 2439 atoms
average map value = 0.3924, steps = 56
shifted from previous position = 2.58
rotated from previous position = 3.16 degrees
atoms outside contour = 68, contour level = 4.74e-05
Position of copy of 7b5k-pdb-bundle2-Ec24Fitted_20250217.pdb (#12) relative to
Ec24ESiteMask_J200_20250225.mrc (#11) coordinates:
Matrix rotation and translation
0.99865636 0.01039049 0.05076931 -14.33679294
-0.01063025 0.99993357 0.00445478 0.97588705
-0.05071965 -0.00498849 0.99870047 13.06843834
Axis -0.09073752 0.97517691 -0.20198192
Axis point 248.69723774 0.00000000 289.66464620
Rotation angle (degrees) 2.98280031
Shift along axis -0.38704077
> fitmap #12 inMap #11
Fit molecule copy of 7b5k-pdb-bundle2-Ec24Fitted_20250217.pdb (#12) to map
Ec24ESiteMask_J200_20250225.mrc (#11) using 2439 atoms
average map value = 0.3924, steps = 44
shifted from previous position = 0.00414
rotated from previous position = 0.0103 degrees
atoms outside contour = 68, contour level = 4.74e-05
Position of copy of 7b5k-pdb-bundle2-Ec24Fitted_20250217.pdb (#12) relative to
Ec24ESiteMask_J200_20250225.mrc (#11) coordinates:
Matrix rotation and translation
0.99866225 0.01023523 0.05068486 -14.27985534
-0.01047632 0.99993503 0.00449329 0.92869965
-0.05063557 -0.00501827 0.99870459 13.05193845
Axis -0.09158752 0.97562196 -0.19943298
Axis point 248.83611343 0.00000000 289.00880815
Rotation angle (degrees) 2.97648340
Shift along axis -0.38907061
> fitmap #12 inMap #11
Fit molecule copy of 7b5k-pdb-bundle2-Ec24Fitted_20250217.pdb (#12) to map
Ec24ESiteMask_J200_20250225.mrc (#11) using 2439 atoms
average map value = 0.3924, steps = 40
shifted from previous position = 0.0171
rotated from previous position = 0.0241 degrees
atoms outside contour = 68, contour level = 4.74e-05
Position of copy of 7b5k-pdb-bundle2-Ec24Fitted_20250217.pdb (#12) relative to
Ec24ESiteMask_J200_20250225.mrc (#11) coordinates:
Matrix rotation and translation
0.99867818 0.01042098 0.05033186 -14.24469794
-0.01066675 0.99993245 0.00461693 0.95161210
-0.05028035 -0.00514770 0.99872188 12.99329217
Axis -0.09456248 0.97434755 -0.20421752
Axis point 249.49765798 0.00000000 290.28034606
Rotation angle (degrees) 2.95952899
Shift along axis -0.37924297
> fitmap #12 inMap #11
Fit molecule copy of 7b5k-pdb-bundle2-Ec24Fitted_20250217.pdb (#12) to map
Ec24ESiteMask_J200_20250225.mrc (#11) using 2439 atoms
average map value = 0.3924, steps = 40
shifted from previous position = 0.021
rotated from previous position = 0.00564 degrees
atoms outside contour = 69, contour level = 4.74e-05
Position of copy of 7b5k-pdb-bundle2-Ec24Fitted_20250217.pdb (#12) relative to
Ec24ESiteMask_J200_20250225.mrc (#11) coordinates:
Matrix rotation and translation
0.99867731 0.01034944 0.05036389 -14.22069139
-0.01059248 0.99993350 0.00456103 0.93644337
-0.05031333 -0.00508848 0.99872052 12.98685006
Axis -0.09342701 0.97476127 -0.20276058
Axis point 249.17508802 0.00000000 289.62972614
Rotation angle (degrees) 2.96018479
Shift along axis -0.39181583
> fitmap #12 inMap #11
Fit molecule copy of 7b5k-pdb-bundle2-Ec24Fitted_20250217.pdb (#12) to map
Ec24ESiteMask_J200_20250225.mrc (#11) using 2439 atoms
average map value = 0.3924, steps = 36
shifted from previous position = 0.000555
rotated from previous position = 0.0207 degrees
atoms outside contour = 68, contour level = 4.74e-05
Position of copy of 7b5k-pdb-bundle2-Ec24Fitted_20250217.pdb (#12) relative to
Ec24ESiteMask_J200_20250225.mrc (#11) coordinates:
Matrix rotation and translation
0.99865946 0.01037971 0.05071032 -14.31274361
-0.01061957 0.99993365 0.00446276 0.96867399
-0.05066063 -0.00499530 0.99870343 13.05291684
Axis -0.09098285 0.97514928 -0.20200494
Axis point 248.68949580 0.00000000 289.51895938
Rotation angle (degrees) 2.97941354
Shift along axis -0.38993771
> fitmap #12 inMap #11
Fit molecule copy of 7b5k-pdb-bundle2-Ec24Fitted_20250217.pdb (#12) to map
Ec24ESiteMask_J200_20250225.mrc (#11) using 2439 atoms
average map value = 0.3924, steps = 36
shifted from previous position = 0.00037
rotated from previous position = 0.00372 degrees
atoms outside contour = 68, contour level = 4.74e-05
Position of copy of 7b5k-pdb-bundle2-Ec24Fitted_20250217.pdb (#12) relative to
Ec24ESiteMask_J200_20250225.mrc (#11) coordinates:
Matrix rotation and translation
0.99865757 0.01033500 0.05075670 -14.31476931
-0.01057473 0.99993415 0.00445682 0.95926938
-0.05070730 -0.00498757 0.99870110 13.06274853
Axis -0.09078900 0.97537390 -0.20100527
Axis point 248.65258444 0.00000000 289.30195505
Rotation angle (degrees) 2.98146346
Shift along axis -0.39041142
> fitmap #12 inMap #11
Fit molecule copy of 7b5k-pdb-bundle2-Ec24Fitted_20250217.pdb (#12) to map
Ec24ESiteMask_J200_20250225.mrc (#11) using 2439 atoms
average map value = 0.3924, steps = 40
shifted from previous position = 0.00157
rotated from previous position = 0.0242 degrees
atoms outside contour = 69, contour level = 4.74e-05
Position of copy of 7b5k-pdb-bundle2-Ec24Fitted_20250217.pdb (#12) relative to
Ec24ESiteMask_J200_20250225.mrc (#11) coordinates:
Matrix rotation and translation
0.99867504 0.01036594 0.05040540 -14.23546211
-0.01061553 0.99993267 0.00468649 0.90973585
-0.05035343 -0.00521536 0.99871784 13.02305405
Axis -0.09576685 0.97450003 -0.20292462
Axis point 249.67222487 0.00000000 289.72869218
Rotation angle (degrees) 2.96338136
Shift along axis -0.39287533
Average map value = 0.3924 for 2439 atoms, 69 outside contour
> fitmap #12 inMap #11
Fit molecule copy of 7b5k-pdb-bundle2-Ec24Fitted_20250217.pdb (#12) to map
Ec24ESiteMask_J200_20250225.mrc (#11) using 2439 atoms
average map value = 0.3924, steps = 40
shifted from previous position = 0.00285
rotated from previous position = 0.024 degrees
atoms outside contour = 68, contour level = 4.74e-05
Position of copy of 7b5k-pdb-bundle2-Ec24Fitted_20250217.pdb (#12) relative to
Ec24ESiteMask_J200_20250225.mrc (#11) coordinates:
Matrix rotation and translation
0.99865815 0.01035085 0.05074206 -14.31342846
-0.01058968 0.99993407 0.00444020 0.96618463
-0.05069276 -0.00497158 0.99870192 13.05522808
Axis -0.09049741 0.97532984 -0.20135026
Axis point 248.57392944 0.00000000 289.35286358
Rotation angle (degrees) 2.98074011
Shift along axis -0.39099667
> fitmap #12 inMap #11
Fit molecule copy of 7b5k-pdb-bundle2-Ec24Fitted_20250217.pdb (#12) to map
Ec24ESiteMask_J200_20250225.mrc (#11) using 2439 atoms
average map value = 0.3924, steps = 40
shifted from previous position = 0.0206
rotated from previous position = 0.0135 degrees
atoms outside contour = 68, contour level = 4.74e-05
Position of copy of 7b5k-pdb-bundle2-Ec24Fitted_20250217.pdb (#12) relative to
Ec24ESiteMask_J200_20250225.mrc (#11) coordinates:
Matrix rotation and translation
0.99866812 0.01042302 0.05053065 -14.29249971
-0.01065710 0.99993368 0.00436520 1.01339693
-0.05048180 -0.00489790 0.99871297 12.99050075
Axis -0.08940910 0.97499043 -0.20346908
Axis point 248.41477104 0.00000000 290.06327333
Rotation angle (degrees) 2.96935166
Shift along axis -0.37723344
> fitmap #12 inMap #11
Fit molecule copy of 7b5k-pdb-bundle2-Ec24Fitted_20250217.pdb (#12) to map
Ec24ESiteMask_J200_20250225.mrc (#11) using 2439 atoms
average map value = 0.3924, steps = 40
shifted from previous position = 0.0024
rotated from previous position = 0.013 degrees
atoms outside contour = 68, contour level = 4.74e-05
Position of copy of 7b5k-pdb-bundle2-Ec24Fitted_20250217.pdb (#12) relative to
Ec24ESiteMask_J200_20250225.mrc (#11) coordinates:
Matrix rotation and translation
0.99867284 0.01033130 0.05045623 -14.25340585
-0.01057493 0.99993367 0.00456395 0.94072712
-0.05040573 -0.00509146 0.99871585 13.01174407
Axis -0.09332739 0.97491301 -0.20207579
Axis point 249.22691891 0.00000000 289.75257784
Rotation angle (degrees) 2.96515929
Shift along axis -0.38199815
> fitmap #12 inMap #11
Fit molecule copy of 7b5k-pdb-bundle2-Ec24Fitted_20250217.pdb (#12) to map
Ec24ESiteMask_J200_20250225.mrc (#11) using 2439 atoms
average map value = 0.3924, steps = 28
shifted from previous position = 0.0255
rotated from previous position = 0.0264 degrees
atoms outside contour = 68, contour level = 4.74e-05
Position of copy of 7b5k-pdb-bundle2-Ec24Fitted_20250217.pdb (#12) relative to
Ec24ESiteMask_J200_20250225.mrc (#11) coordinates:
Matrix rotation and translation
0.99865103 0.01030764 0.05089081 -14.33503476
-0.01054599 0.99993463 0.00441728 0.95828247
-0.05084195 -0.00494802 0.99869445 13.08716294
Axis -0.08981820 0.97567093 -0.19999734
Axis point 248.43523009 0.00000000 288.96445188
Rotation angle (degrees) 2.98845705
Shift along axis -0.39488229
> ui mousemode right "translate selected models"
> select add #12
2439 atoms, 2628 bonds, 76 residues, 1 model selected
> view matrix models
> #12,0.99848,-0.0085185,0.054406,-10.961,0.0082836,0.99996,0.0045408,-6.0648,-0.054443,-0.0040832,0.99851,18.788
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.9975,-0.039534,0.058614,-5.3368,0.039405,0.99922,0.0033623,-12.832,-0.058701,-0.0010442,0.99828,19.201
> view matrix models
> #12,0.98824,-0.14607,-0.045249,46.021,0.14876,0.98686,0.063054,-51.116,0.035444,-0.069043,0.99698,11.895
> view matrix models
> #12,0.98767,-0.15588,0.014481,32.72,0.15202,0.97705,0.1492,-72.156,-0.037406,-0.14516,0.9887,46.877
> view matrix models
> #12,0.9085,-0.41273,-0.065465,125.55,0.41696,0.88483,0.2079,-129.61,-0.02788,-0.21617,0.97596,62.821
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.9085,-0.41273,-0.065465,128.33,0.41696,0.88483,0.2079,-129.43,-0.02788,-0.21617,0.97596,62.98
> close #12
> volume resample #11 onGrid #7
Opened Ec24ESiteMask_J200_20250225.mrc resampled as #12, grid size
448,448,448, pixel 1.18, shown at step 1, values float32
> close #11
> save "C:/Users/jlerath/Desktop/Ec24
> CryoEM/Masks/Ec24ESiteMask_J200_20250225.mrc" models #12
> hide #!12 models
> open "C:/Users/jlerath/Desktop/Ec24
> CryoEM/J137/J200_004_volume_map_APEdeepemhancer2.mrc"
Opened J200_004_volume_map_APEdeepemhancer2.mrc as #11, grid size 448,448,448,
pixel 1.18, shown at level 0.000137, step 2, values float32
> volume #11 step 1
> volume #11 level 0.15
> volume #11 level 0.2
> surface dust #11 size 11.8
> surface dust #11 size 20
> surface dust #11 size 50
> show #!9 models
> hide #!9 models
> show #!12 models
> show #!9 models
> hide #!12 models
> show #!12 models
> hide #!9 models
> transparency #12 50
> volume #12 level 0.08833
> volume #12 level 0.1122
> volume #12 level 0.129
> show #!7 models
> color #7 #ffff7fff models
> volume #12 level 0.115
> hide #!7 models
> show #!9 models
> volume #9 level 0.1496
> volume #12 style mesh
> volume #9 style mesh
> volume #12 level 0.1906
> hide #!9 models
> volume #12 level 0.2593
> volume #12 level 0.2803
> volume #12 level 0.3
> volume #12 level 0.25
> volume mask #12 surfaces #11 fullMap true pad 0.25 extend 1
Opened Ec24ESiteMask_J200_20250225.mrc masked as #13, grid size 448,448,448,
pixel 1.18, shown at step 1, values float32
> hide #!11 models
> volume #13 style surface
> volume #13 color #009e7380
> transparency #13 0
> show #!12 models
> show #!11 models
> hide #!12 models
> show #!12 models
> volume mask #12 surfaces #11 fullMap true pad 0.25 extend 1
Opened Ec24ESiteMask_J200_20250225.mrc masked as #14, grid size 448,448,448,
pixel 1.18, shown at step 1, values float32
> close #13
> hide #!11 models
> volume #14 style surface
> transparency #14 0
> show #!11 models
> hide #!11 models
> volume #14 level 0.2234
> volume #14 level 0.25
> show #!11 models
> hide #!11 models
> show #!7 models
> hide #!7 models
> show #!6 models
> hide #!14 models
> show #!14 models
> show #!7 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!7 models
> hide #!14 models
> show #!12 models
> volume #14 level 0.1477
> volume #14 level 0.25
> volume #12 level 0.08605
> volume #12 level 0.05942
> show #!14 models
> volume #12 level 0.006174
> volume subtract #6 #12
Opened volume difference as #13, grid size 448,448,448, pixel 1.18, shown at
step 1, values float32
> hide #!14 models
> surface dust #13 size 11.8
> show #!14 models
> hide #!14 models
> show #!12 models
> show #!11 models
> hide #!11 models
> show #!10 models
> hide #!10 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!13 models
> hide #!9 models
> hide #!12 models
> open "C:/Users/jlerath/Desktop/Ec24
> CryoEM/J150/J150_004_volume_map_deepemhancer_modified_nodust_20250219.mrc"
Opened J150_004_volume_map_deepemhancer_modified_nodust_20250219.mrc as #15,
grid size 197,185,155, pixel 1.18,1.18,1.18, shown at level 0.654, step 1,
values float32
> open "C:/Users/jlerath/Desktop/Ec24
> CryoEM/J150/J150_004_volume_map_deepemhancer2_nodust.mrc"
Opened J150_004_volume_map_deepemhancer2_nodust.mrc as #16, grid size
448,448,448, pixel 1.18, shown at level 0.000109, step 2, values float32
> volume #16 level 0.2526
> volume #15 level 0.25
> volume #16 step 1
> hide #!16 models
> volume #15 level 0.03173
> volume #15 level 0.03
> show #!16 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> open "C:/Users/jlerath/Desktop/Ec24
> CryoEM/J150/J150_004_volume_map_deepemhancer2.mrc"
Opened J150_004_volume_map_deepemhancer2.mrc as #17, grid size 448,448,448,
pixel 1.18, shown at level -0.00277, step 2, values float32
> hide #!15 models
> hide #!16 models
> volume #17 step 1
> volume #17 level 0.0143
> volume #17 level 0.01
> surface dust #17 size 11.8
> color #17 #0072b2ff models
> color #17 #56b4e9ff models
> volume #17 level 0.02
> volume #17 level 0.25
> volume #17 level 0.02
> volume mask #17 surfaces #17 fullMap true pad 0.25 extend 1
Opened J150_004_volume_map_deepemhancer2.mrc masked as #18, grid size
448,448,448, pixel 1.18, shown at step 1, values float32
> volume #17 level 0.1
> volume #17 level 0.01
> volume #17 level 0.25
> volume #17 level 0.02
> volume #18 level 0.1
> volume #18 level 0.25
> surface dust #18 size 11.8
> volume #18 level 0.15
> surface dust #18 size 11.8
> volume #18 level 0.1
> hide #!18 models
> show #!17 models
> volume #18 level 0.02
> volume #18 level 0.25
> color #16 #0072b2ff models
> show #!16 models
> hide #!18 models
> show #!18 models
> volume #18 level 0.02
> volume #16 level 0.25
> hide #!16 models
> show #!16 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> close #16
> save "C:/Users/jlerath/Desktop/Ec24
> CryoEM/J150/J150_004_volume_map_deepemhancer2_nodust.mrc" models #18
> volume #18 level 0.25
> show #!17 models
> close #15
> close #17
> close #18
> show #!13 models
> show #!14 models
> hide #!14 models
> show #!14 models
> volume #14 level 0.3004
> volume #14 level 0.25
> volume #14 level 0.01318
> show #!11 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> volume #11 level 0.01898
> volume #12 level 0.01458
> volume #14 level 0.019
> volume #11 level 0.02
> volume #11 level 0.25
> volume #14 level 0.25
> hide #!14 models
> volume #13 level 0.25
> volume #13 level 0.04388
> volume #13 level 0.2
> volume #13 level 0.02
> volume #13 level 0.05
> volume #13 level 0.25
> volume #13 level 0.2
> show #!14 models
> hide #!14 models
> hide #!13 models
> show #!13 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> volume mask #13 surfaces #13 fullMap true pad 0.25 extend 1
Opened volume difference masked as #15, grid size 448,448,448, pixel 1.18,
shown at step 1, values float32
> save "C:/Users/jlerath/Desktop/Ec24
> CryoEM/J137/J200_004_volume_map_deepemhancer2_tRNASubtracted_nodust.mrc"
> models #15
> close #13
> show #!14 models
> save "C:/Users/jlerath/Desktop/Ec24
> CryoEM/J137/J200_004_volume_map_Esitedeepemhancer2_filtered.mrc" models #14
> close #12
> close #11
> close #9-10,14
> show #!8 models
> close #8
> show #!7 models
> close #1-7,15
> open "C:/Users/jlerath/Desktop/Ec24
> CryoEM/J138/cryosparc_P49_J209_003_volume_map_sharp.mrc"
Opened cryosparc_P49_J209_003_volume_map_sharp.mrc as #1, grid size
448,448,448, pixel 1.18, shown at level 0.206, step 2, values float32
> open "C:/Users/jlerath/Desktop/Ec24
> CryoEM/J138/cryosparc_P49_J210_004_volume_map_sharp.mrc"
Opened cryosparc_P49_J210_004_volume_map_sharp.mrc as #2, grid size
448,448,448, pixel 1.18, shown at level 0.114, step 2, values float32
> open "C:/Users/jlerath/Desktop/Ec24
> CryoEM/J138/cryosparc_P49_J211_005_volume_map_sharp.mrc"
Opened cryosparc_P49_J211_005_volume_map_sharp.mrc as #3, grid size
448,448,448, pixel 1.18, shown at level 0.108, step 2, values float32
> surface dust #1-3 size 10
> surface dust #1-3 size 5
> surface dust #1-3 size 8
> surface dust #1-3 size 10
> volume #1-3 step 1
> close #1-3
> open "C:/Users/jlerath/Desktop/Ec24
> CryoEM/J137/cryosparc_P49_J200_004_volume_map_sharp.mrc"
> "C:/Users/jlerath/Desktop/Ec24
> CryoEM/J137/cryosparc_P49_J198_003_volume_map_sharp.mrc"
> "C:/Users/jlerath/Desktop/Ec24
> CryoEM/J137/cryosparc_P49_J199_004_volume_map_sharp.mrc"
Opened cryosparc_P49_J200_004_volume_map_sharp.mrc as #1.1, grid size
448,448,448, pixel 1.18, shown at level 0.124, step 2, values float32
Opened cryosparc_P49_J198_003_volume_map_sharp.mrc as #1.2, grid size
448,448,448, pixel 1.18, shown at level 0.204, step 2, values float32
Opened cryosparc_P49_J199_004_volume_map_sharp.mrc as #1.3, grid size
448,448,448, pixel 1.18, shown at level 0.132, step 2, values float32
> open "C:/Users/jlerath/Desktop/Ec24
> CryoEM/J137/J200_004_volume_map_Esitedeepemhancer2_filtered.mrc"
> "C:/Users/jlerath/Desktop/Ec24
> CryoEM/J137/J200_004_volume_map_deepemhancer2_tRNASubtracted_nodust.mrc"
> "C:/Users/jlerath/Desktop/Ec24
> CryoEM/J137/J200_004_volume_map_Esitedeepemhancer2.mrc"
> "C:/Users/jlerath/Desktop/Ec24
> CryoEM/J137/J200_004_volume_map_deepemhancer2_nodust.mrc"
> "C:/Users/jlerath/Desktop/Ec24
> CryoEM/J137/J199_004_volume_map_deepemhancer2_nodust.mrc"
> "C:/Users/jlerath/Desktop/Ec24
> CryoEM/J137/J198_003_volume_map_deepemhancer2_nodust.mrc"
Opened J200_004_volume_map_Esitedeepemhancer2_filtered.mrc as #2.1, grid size
448,448,448, pixel 1.18, shown at level 4.7e-05, step 2, values float32
Opened J200_004_volume_map_deepemhancer2_tRNASubtracted_nodust.mrc as #2.2,
grid size 448,448,448, pixel 1.18, shown at level 0.000231, step 2, values
float32
Opened J200_004_volume_map_Esitedeepemhancer2.mrc as #2.3, grid size
448,448,448, pixel 1.18, shown at level 0.000137, step 2, values float32
Opened J200_004_volume_map_deepemhancer2_nodust.mrc as #2.4, grid size
448,448,448, pixel 1.18, shown at level 5.65e-05, step 2, values float32
Opened J199_004_volume_map_deepemhancer2_nodust.mrc as #2.5, grid size
448,448,448, pixel 1.18, shown at level 3.61e-05, step 2, values float32
Opened J198_003_volume_map_deepemhancer2_nodust.mrc as #2.6, grid size
448,448,448, pixel 1.18, shown at level 0.00011, step 2, values float32
> surface dust #1 size 10
> hide #!2 models
> volume #1 step 1
> show #!2 models
> hide #!2.6 models
> show #!2.6 models
> hide #!2.6 models
> show #!2.6 models
> volume #2 step 1
> volume #2.6 level 0.2
> volume #2.4,2.5 level 0.2
No volumes specified
> volume #2.4, 2.5 level 0.2
No volumes specified
> volume #2.4, #2.5 level 0.2
Expected a density maps specifier or a keyword
> volume #2.4 level 0.2
> volume #2.5 level 0.2
> hide #!2.5 models
> hide #!2.4 models
> hide #!2.2 models
> show #!2.2 models
> volume #2.2 level 0.2
> volume #2.3 level 0.25
> volume #2.3 level 0.2
> volume #2.1 level 0.2
> hide #!1.2 models
> hide #!2.6 models
> hide #!2.2 models
> show #!2.2 models
> hide #!2.2 models
> show #!2.2 models
> show #!2.6 models
> color #2.6 #0072b2ff models
> color #1.2 #0072b2ff models
> show #!1.2 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.2 models
> color #2.5 #f0e442ff models
> color #2.4 #f0e442ff models
> color #2.3 #009e73ff models
> color #2.1 #009e73ff models
> color #2.2 #f0e442ff models
> color #1.3 #f0e442ff models
> color #1.1 #f0e442ff models
> hide #!1.1 models
> hide #!1 models
> hide #!2.3 models
> show #!2.3 models
> hide #!1.3 models
> show #!1.3 models
> hide #!1.3 models
> hide #!2.2 models
> show #!2.2 models
> hide #!2.1 models
> show #!2.1 models
> hide #!2.1 models
> show #!2.1 models
> hide #!2.3 models
> volume #2.6 level 0.25
> surface dust #2.1 size 11.8
> surface dust #2.2 size 11.8
> surface dust #2.6 size 11.8
> volume #2.6 level 0.2
> surface dust #2.6 size 5
> surface dust #2.6 size 10
> surface dust #2.6 size 50
> surface dust #2.6 size 0
[Repeated 1 time(s)]
> volume #2.6 level 0.25
> surface dust #2.1 size 11.8
> surface dust #2.2 size 11.8
> surface dust #2.6 size 11.8
> surface dust #2.6 size 0
> surface dust #2.1 size 11.8
> surface dust #2.2 size 11.8
> surface dust #2.6 size 11.8
> volume gaussian #2.6 sDev 2
Opened J198_003_volume_map_deepemhancer2_nodust.mrc gaussian as #3, grid size
448,448,448, pixel 1.18, shown at step 1, values float32
> hide #!2 models
> volume #3 level 0.009606
> ui tool show "Segment Map"
Segmenting J198_003_volume_map_deepemhancer2_nodust.mrc gaussian, density
threshold 0.009606
Showing 161 region surfaces
2389 watershed regions, grouped to 161 regions
Showing J198_003_volume_map_deepemhancer2_nodust gaussian.seg - 161 regions,
161 surfaces
> show #!2.6 models
> hide #!3 models
> transparency #4 25
> transparency #4 50
> ui mousemode right select
> select #4.61
1 model selected
> select #4.28
1 model selected
> select add #4.61
2 models selected
> select add #4.9
3 models selected
> select add #4.11
4 models selected
> select add #4.85
5 models selected
> select add #4.80
6 models selected
> select add #4.134
7 models selected
> select add #4.65
8 models selected
> select add #4.76
9 models selected
> select add #4.77
10 models selected
> select add #4.18
11 models selected
> select add #4.122
12 models selected
> select add #4.31
13 models selected
Grouped 13 regions
> select #4.56
1 model selected
> select add #4.14
2 models selected
> select add #4.40
3 models selected
> select add #4.53
4 models selected
> select add #4.144
5 models selected
> select add #4.7
6 models selected
> select add #4.19
7 models selected
> select add #4.104
8 models selected
> select add #4.32
9 models selected
Grouped 9 regions
Ungrouped to 9 regions
> select add #4.113
10 models selected
> select add #4.112
11 models selected
Grouped 11 regions
> hide #!2.2 models
> hide #!2.1 models
> select #4.7
1 model selected
Ungrouped to 11 regions
> select add #4.153
12 models selected
Grouped 12 regions
> select clear
> hide #!4 models
> hide #!2.6 models
> open "C:/Users/jlerath/Desktop/Ec24
> CryoEM/J138/J209_003_volume_map_deepemhancer2.mrc"
> "C:/Users/jlerath/Desktop/Ec24
> CryoEM/J138/J211_005_volume_map_deepemhancer2.mrc"
> "C:/Users/jlerath/Desktop/Ec24
> CryoEM/J138/J210_004_volume_map_deepemhancer2.mrc"
Opened J209_003_volume_map_deepemhancer2.mrc as #5.1, grid size 448,448,448,
pixel 1.18, shown at level 0.0604, step 2, values float32
Opened J211_005_volume_map_deepemhancer2.mrc as #5.2, grid size 448,448,448,
pixel 1.18, shown at level 0.0316, step 2, values float32
Opened J210_004_volume_map_deepemhancer2.mrc as #5.3, grid size 448,448,448,
pixel 1.18, shown at level 0.0211, step 2, values float32
> volume #5 step 1
> volume #5 level 0.2
> surface dust #5 size 10
> surface dust #5 size 15
> surface dust #5 size 25
> volume #5 level 0.25
> hide #!5.1 models
> surface dust #5.2 size 35
> surface dust #5.2 size 25
> surface dust #5.2 size 30
> surface dust #5.2 size 26
> surface dust #5.2 size 27
> surface dust #5.2 size 20
> surface dust #5.2 size 25
> hide #!5 models
> show #!4 models
> show #!3 models
> hide #!3 models
> show #!2.6 models
> select #4.9
1 model selected
> select #4.7
1 model selected
Saving 1 regions to mrc file...
Opened J198_003_volume_map_deepemhancer2_leftwing_mask.mrc as #6, grid size
79,118,85, pixel 1.18, shown at step 1, values float32
Wrote J198_003_volume_map_deepemhancer2_leftwing_mask.mrc
> select #4.9
1 model selected
Saving 138 regions to mrc file...
Opened J198_003_volume_map_deepemhancer2_rightwing_mask.mrc as #7, grid size
202,194,164, pixel 1.18, shown at step 1, values float32
Wrote J198_003_volume_map_deepemhancer2_rightwing_mask.mrc
> hide #!4 models
> hide #!2.6 models
> volume #7 level 0.0151
> volume #6 level 0.01217
> close #7
> show #!4 models
> select clear
> select #4.9
1 model selected
Saving 1 regions to mrc file...
Opened J198_003_volume_map_deepemhancer2_rightwing_mask.mrc as #7, grid size
88,91,108, pixel 1.18, shown at step 1, values float32
Wrote J198_003_volume_map_deepemhancer2_rightwing_mask.mrc
> hide #!4 models
> volume #7 level 0.01254
> volume resample #6-7 onGrid #2.6
Opened J198_003_volume_map_deepemhancer2_leftwing_mask.mrc resampled as #8,
grid size 448,448,448, pixel 1.18, shown at step 1, values float32
Opened J198_003_volume_map_deepemhancer2_rightwing_mask.mrc resampled as #9,
grid size 448,448,448, pixel 1.18, shown at step 1, values float32
> hide #!4 models
> select clear
> save "C:/Users/jlerath/Desktop/Ec24
> CryoEM/Masks/J198_003_volume_map_deepemhancer2_leftwing_mask.mrc" models #8
> close #6-7
> save "C:/Users/jlerath/Desktop/Ec24
> CryoEM/Masks/J198_003_volume_map_deepemhancer2_rightwing_mask.mrc" models #9
> save "C:/Users/jlerath/Desktop/Ec24
> CryoEM/Masks/Ec2450SWingsMaskCreation_20250227.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 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 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 304, in msgpack._cmsgpack.Packer.pack
MemoryError
MemoryError
File "msgpack\\\\_packer.pyx", line 304, in msgpack._cmsgpack.Packer.pack
See log for complete Python traceback.
OpenGL version: 3.3.14761 Core Profile Forward-Compatible Context 21.30.18.11 30.0.13018.11001
OpenGL renderer: AMD Radeon RX 640
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows
Manufacturer: Dell Inc.
Model: OptiPlex 7000
OS: Microsoft Windows 10 Enterprise (Build 19045)
Memory: 34,033,348,608
MaxProcessMemory: 137,438,953,344
CPU: 20 12th Gen Intel(R) Core(TM) i7-12700
OSLanguage: en-US
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
asttokens: 3.0.0
auditwheel: 6.1.0
autocommand: 2.2.2
babel: 2.16.0
backports.tarfile: 1.2.0
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-Clipper: 0.23.0
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-ISOLDE: 1.8.dev0
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
importlib_metadata: 8.0.0
importlib_resources: 6.4.0
inflect: 7.3.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jaraco.context: 5.3.0
jaraco.functools: 4.0.1
jaraco.text: 3.12.1
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
more-itertools: 10.3.0
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
ordered-set: 4.1.0
packaging: 23.2
packaging: 24.1
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
platformdirs: 4.2.2
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
tomli: 2.0.1
tornado: 6.4.2
traitlets: 5.14.3
typeguard: 4.3.0
typing_extensions: 4.12.2
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: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
WMI: 1.5.1
zipp: 3.19.2
Change History (2)
comment:1 by , 8 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Sessions |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → MemoryError saving maps in sessions |
comment:2 by , 8 months ago
| Resolution: | → limitation |
|---|---|
| Status: | assigned → closed |
Out of memory saving a session with many maps.
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