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Opened 2 weeks ago
Closed 10 days ago
#19850 closed defect (limitation)
MemoryError saving session with maps
| 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-10-10.0.26200
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/TM1.cxs
Opened 9ZLK.mrc as #1, grid size 384,384,384, pixel 0.93, shown at level
0.111, step 1, values float32
Log from Tue Feb 10 15:38:26 2026 Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> "C:/Users/mbash/OneDrive/Desktop/MgtA_paper/images_for_paper/deposited_pdb_maps/Deposited_pdbs
> Map_and coordinates_with_code/9ZLK.mrc"
> "C:/Users/mbash/OneDrive/Desktop/MgtA_paper/images_for_paper/deposited_pdb_maps/Deposited_pdbs
> Map_and coordinates_with_code/9ZLK.pdb"
Opened 9ZLK.mrc as #1, grid size 384,384,384, pixel 0.93, shown at level
0.0178, step 2, values float32
Chain information for 9ZLK.pdb #2
---
Chain | Description
A | No description available
> ui tool show "Hide Dust"
> surface dust #1 size 21.17
[Repeated 1 time(s)]
> ui tool show Toolbar
> volume #1 step 1
> volume #1 level 0.1052
> backgound colour white
Unknown command: backgound colour white
> set bgColor white
> volume #1 style mesh
> hide cartoons
> hide atoms
[Repeated 1 time(s)]
> show atoms
> select 72-105
Expected an objects specifier or a keyword
> select 73-106
Expected an objects specifier or a keyword
> select :73-106
269 atoms, 274 bonds, 34 residues, 1 model selected
> preset "overall look" interactive
Using preset: Overall Look / Interactive
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
lighting depthCue t
> preset "overall look" interactive
Using preset: Overall Look / Interactive
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
lighting depthCue t
> select up
394 atoms, 401 bonds, 51 residues, 1 model selected
> select up
7167 atoms, 7288 bonds, 897 residues, 1 model selected
> set bgColor white
> select :73-106
269 atoms, 274 bonds, 34 residues, 1 model selected
> select :107-910
6414 atoms, 6524 bonds, 804 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select :22-910
7110 atoms, 7225 bonds, 894 residues, 1 model selected
> hide sel atoms
> select :73-106
269 atoms, 274 bonds, 34 residues, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 5.58
> volume #1 level 0.1475
> ui tool show "Surface Zone"
> surface zone #1 nearAtoms #2 distance 5.58
> surface zone #1 nearAtoms #2 distance 3.52
> volume zone #1 nearAtoms sel & #2 range 5.58
> surface zone #1 nearAtoms #2 distance 1.95
> volume zone #1 nearAtoms sel & #2 range 5.58
> volume #1 level 0.1869
> volume #1 near Atoms sel  range
Expected a keyword
> volume zone #1 nearAtoms sel & #2 range 4
> volume zone #1 nearAtoms sel & #2 range 3
> volume #1 level 0.1362
> volume zone #1 nearAtoms sel & #2 range 2.5
> volume #1 level 0.08825
> transparency 50
> transparency 0
> transparency 50
> volume style image
> volume style mesh
> volume style image
> volume style mesh
> select ::name="HOH"
26 atoms, 26 residues, 1 model selected
> hide sel atoms
> select ::name="K"
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select ::name="MG"
4 atoms, 4 residues, 1 model selected
> hide sel atoms
> select ::name="ACP"
48 atoms, 50 bonds, 1 residue, 1 model selected
> hide sel atoms
> graphics silhouettes true
> lighting shadows true
> lighting flat
> lighting full
> lighting soft
> lighting simple
[Repeated 1 time(s)]
> lighting soft
> lighting full
> lighting flat
> graphics silhouettes false
> lighting simple
> save
> C:/Users/mbash/OneDrive/Desktop/MgtA_paper/images_for_paper/TM1_Map_simple.png
> width 1981 height 1285 supersample 3
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/TM1_Map_simple.png
> width 1981 height 1285 supersample 3 transparentBackground true
> lighting full
[Repeated 1 time(s)]
> lighting simple
> lighting full
> lighting simple
> lighting full
> lighting simple
> lighting full
> lighting soft
> lighting flat
> lighting shadows true intensity 0.5
> lighting full
> lighting soft
> lighting simple
> lighting soft
> volume #1 change image level -0.005576,0 level 0.01764,0.8 level 0.9387,1
> volume #1 level 0.1108
> lighting flat
> lighting full
[Repeated 1 time(s)]
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/TM1_Map_full.png
> width 1981 height 1285 supersample 3 transparentBackground true
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/TM1.cxs includeMaps
> true
——— End of log from Tue Feb 10 15:38:26 2026 ———
opened ChimeraX session
> select :73-106
269 atoms, 274 bonds, 34 residues, 1 model selected
> volume #1 color #00000080
> ui tool show Toolbar
> graphics silhouettes false
> view sel
> volume zone #1 nearAtoms sel & #2 range 2.0
> view sel
[Repeated 1 time(s)]
> select add #2
7246 atoms, 7338 bonds, 929 residues, 1 model selected
> select subtract #2
Nothing selected
> save
> C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/TM1_Map_simple_scale.png
> width 3000 height 2694 supersample 3 transparentBackground true
> select :73-106
269 atoms, 274 bonds, 34 residues, 1 model selected
> view
> select :14-910, Mg, HOH, BEF
7197 atoms, 7288 bonds, 927 residues, 1 model selected
> hide sel atoms
> select :73-106
269 atoms, 274 bonds, 34 residues, 1 model selected
> show sel atoms
> select add #2
7246 atoms, 7338 bonds, 929 residues, 1 model selected
> select subtract #2
Nothing selected
> save
> C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/TM1_Map_simple_scale.png
> width 3000 height 2694 supersample 3 transparentBackground true
> color #2#1.1#!1 byelement
> select add #1
3 models selected
> color #1.1 gray
> select clear
> select add #1
3 models selected
> color #1.1 dim gray
> select clear
> select /A:108-135
218 atoms, 219 bonds, 28 residues, 1 model selected
> show sel target ab
> select clear
[Repeated 1 time(s)]
> hide #2#1.1#!1 target a
> select /A:108-135
218 atoms, 219 bonds, 28 residues, 1 model selected
> show sel atoms
> select up
243 atoms, 245 bonds, 32 residues, 1 model selected
> select up
7167 atoms, 7288 bonds, 897 residues, 1 model selected
> select clear
> select /A:108-135
218 atoms, 219 bonds, 28 residues, 1 model selected
> volume zone #1 nearAtoms sel & #2 range 2.0
> select clear
[Repeated 1 time(s)]
> hide atoms
> select /A:675-716
326 atoms, 330 bonds, 42 residues, 1 model selected
> show sel atoms
> select up
383 atoms, 390 bonds, 49 residues, 1 model selected
> select up
7167 atoms, 7288 bonds, 897 residues, 1 model selected
> select clear
> select /A:675-716
326 atoms, 330 bonds, 42 residues, 1 model selected
> select clear
> select /A:675-716
326 atoms, 330 bonds, 42 residues, 1 model selected
> volume zone #1 nearAtoms sel & #2 range 2.0
> view name TM5
> select clear
> select ~sel & ##selected
Nothing selected
> view name TM5large
> view TM5
> select ~sel & ##selected
Nothing selected
> view TM5large
> select ~sel & ##selected
Nothing selected
> view TM5
> select ~sel & ##selected
Nothing selected
> view TM5large
> view list
Named views: TM5, TM5large
> view TM5
> view TM5large
> view TM5
> view TM5large
> view TM5
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/new_view.cxs
> includeMaps true
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/TM5_best.png width
> 3000 height 1960 supersample 3 transparentBackground true
> select /A:675-716
326 atoms, 330 bonds, 42 residues, 1 model selected
> select /A:675-716
326 atoms, 330 bonds, 42 residues, 1 model selected
> select /A:73-106
269 atoms, 274 bonds, 34 residues, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> select /A:675-716
326 atoms, 330 bonds, 42 residues, 1 model selected
> hide sel atoms
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/TM1_best.png width
> 3000 height 1960 supersample 3 transparentBackground true
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/TM1_best.cxs
> includeMaps true
> select /A:675-716
326 atoms, 330 bonds, 42 residues, 1 model selected
> select /A:73-106
269 atoms, 274 bonds, 34 residues, 1 model selected
> hide sel atoms
> select /A:108-135
218 atoms, 219 bonds, 28 residues, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> select add #2
7246 atoms, 7338 bonds, 929 residues, 1 model selected
> select subtract #2
Nothing selected
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/TM2_best.png width
> 3000 height 1960 supersample 3 transparentBackground true
> select /A:108-135
218 atoms, 219 bonds, 28 residues, 1 model selected
> hide sel atoms
> select /A:268-299
263 atoms, 270 bonds, 32 residues, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> select add #2
7246 atoms, 7338 bonds, 929 residues, 1 model selected
> select subtract #2
Nothing selected
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/TM3_best.png width
> 3000 height 1960 supersample 3 transparentBackground true
> select /A:302-340
280 atoms, 284 bonds, 39 residues, 1 model selected
> show sel atoms
> select /A:268-299
263 atoms, 270 bonds, 32 residues, 1 model selected
> hide sel atoms
> select /A:302-340
280 atoms, 284 bonds, 39 residues, 1 model selected
> volume zone #1 nearAtoms sel & #2 range 2.0
> select add #2
7246 atoms, 7338 bonds, 929 residues, 1 model selected
> select subtract #2
Nothing selected
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/TM4_best.png width
> 3000 height 1960 supersample 3 transparentBackground true
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/TM4_best_1.png
> width 3000 height 1960 supersample 3 transparentBackground true
> select /A:302-340
280 atoms, 284 bonds, 39 residues, 1 model selected
> hide sel atoms
> select /A:675-716
326 atoms, 330 bonds, 42 residues, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> select add #2
7246 atoms, 7338 bonds, 929 residues, 1 model selected
> select subtract #2
Nothing selected
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/TM5_best_1.png
> width 3000 height 1960 supersample 3 transparentBackground true
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/TM5_best_2.png
> width 3000 height 1960 supersample 3 transparentBackground true
> select /A:675-716
326 atoms, 330 bonds, 42 residues, 1 model selected
> hide sel atoms
> select /A:675-716
326 atoms, 330 bonds, 42 residues, 1 model selected
> show sel atoms
> select /A:675-716, Mg
326 atoms, 330 bonds, 42 residues, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> show sel cartoons
> hide sel cartoons
> show sel cartoons
[Repeated 1 time(s)]
> hide sel cartoons
> show sel surfaces
> hide sel surfaces
> select /A:675-716, Mg
326 atoms, 330 bonds, 42 residues, 1 model selected
> show sel atoms
> select :675-716, Mg
330 atoms, 330 bonds, 46 residues, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> select add #2
7246 atoms, 7338 bonds, 929 residues, 2 models selected
> select subtract #2
1 model selected
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/TM5_best_Mg.png
> width 3000 height 1960 supersample 3 transparentBackground true
> select :675-716, Mg
330 atoms, 330 bonds, 46 residues, 1 model selected
> hide sel atoms
> select :718-742
199 atoms, 205 bonds, 25 residues, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> select add #2
7246 atoms, 7338 bonds, 929 residues, 2 models selected
> select subtract #2
1 model selected
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/TM6_best.png width
> 3000 height 1960 supersample 3 transparentBackground true
> select :718-742
199 atoms, 205 bonds, 25 residues, 1 model selected
> hide sel atoms
> select :758-794
287 atoms, 296 bonds, 37 residues, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> select :758-794, Mg
291 atoms, 296 bonds, 41 residues, 1 model selected
> select :758-794, Mg
291 atoms, 296 bonds, 41 residues, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> select add #2
7246 atoms, 7338 bonds, 929 residues, 2 models selected
> select subtract #2
1 model selected
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/TM7_best.png width
> 3000 height 1960 supersample 3 transparentBackground true
> select :799-833, Mg
286 atoms, 292 bonds, 39 residues, 1 model selected
> select :758-794, Mg
291 atoms, 296 bonds, 41 residues, 1 model selected
> hide sel atoms
> select :799-833, Mg
286 atoms, 292 bonds, 39 residues, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> select add #2
7246 atoms, 7338 bonds, 929 residues, 2 models selected
> select subtract #2
1 model selected
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/TM8_best.png width
> 3000 height 1960 supersample 3 transparentBackground true
> select :799-833, Mg
286 atoms, 292 bonds, 39 residues, 1 model selected
> hide sel atoms
> select :845-868
176 atoms, 180 bonds, 24 residues, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> select add #2
7246 atoms, 7338 bonds, 929 residues, 2 models selected
> select subtract #2
1 model selected
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/TM9_best.png width
> 3000 height 1960 supersample 3 transparentBackground true
> select :845-868
176 atoms, 180 bonds, 24 residues, 1 model selected
> hide sel atoms
> select :877-908
274 atoms, 284 bonds, 32 residues, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> select add #2
7246 atoms, 7338 bonds, 929 residues, 2 models selected
> select subtract #2
1 model selected
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/TM10_best.png width
> 3000 height 1960 supersample 3 transparentBackground true
> select :877-908
274 atoms, 284 bonds, 32 residues, 1 model selected
> hide sel atoms
> select :73-106
269 atoms, 274 bonds, 34 residues, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> select add #2
7246 atoms, 7338 bonds, 929 residues, 2 models selected
> select subtract #2
1 model selected
> select :73
6 atoms, 5 bonds, 1 residue, 1 model selected
> select :73-106
269 atoms, 274 bonds, 34 residues, 1 model selected
> hide sel atoms
> select :108-135
218 atoms, 219 bonds, 28 residues, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> select :108
4 atoms, 3 bonds, 1 residue, 1 model selected
> select :108-109
13 atoms, 12 bonds, 2 residues, 1 model selected
> select :108-135
218 atoms, 219 bonds, 28 residues, 1 model selected
> hide sel atoms
> select :268-299
263 atoms, 270 bonds, 32 residues, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> select :268
7 atoms, 6 bonds, 1 residue, 1 model selected
> select :26270
Nothing selected
> select :26-270
1884 atoms, 1906 bonds, 246 residues, 1 model selected
> select :268-270
27 atoms, 27 bonds, 3 residues, 1 model selected
> select :268-299
263 atoms, 270 bonds, 32 residues, 1 model selected
> hide sel atoms
> select :302-340
280 atoms, 284 bonds, 39 residues, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> select :302-305
36 atoms, 37 bonds, 4 residues, 1 model selected
> select :302-340
280 atoms, 284 bonds, 39 residues, 1 model selected
> hide sel atoms
> select :675-716
326 atoms, 330 bonds, 42 residues, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> select :675-680
49 atoms, 48 bonds, 6 residues, 1 model selected
> select :675-699
203 atoms, 204 bonds, 25 residues, 1 model selected
> select :675-750
608 atoms, 622 bonds, 76 residues, 1 model selected
> hide sel atoms
> select :718-742
199 atoms, 205 bonds, 25 residues, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> select :718-720
26 atoms, 27 bonds, 3 residues, 1 model selected
> select :718-800
670 atoms, 694 bonds, 83 residues, 1 model selected
> hide sel atoms
> select :758-794
287 atoms, 296 bonds, 37 residues, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> select :758-765
58 atoms, 58 bonds, 8 residues, 1 model selected
> select :758-800
333 atoms, 344 bonds, 43 residues, 1 model selected
> hide sel atoms
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> select :799-805
42 atoms, 42 bonds, 7 residues, 1 model selected
> select add #2
7246 atoms, 7338 bonds, 929 residues, 2 models selected
> select subtract #2
1 model selected
> select :799-805
42 atoms, 42 bonds, 7 residues, 1 model selected
> select :1-910
7198 atoms, 7288 bonds, 928 residues, 1 model selected
> hide sel atoms
> select :799-833
282 atoms, 292 bonds, 35 residues, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> select :799-805
42 atoms, 42 bonds, 7 residues, 1 model selected
> select :799-900
810 atoms, 837 bonds, 102 residues, 1 model selected
> hide sel atoms
> select :845-865
155 atoms, 158 bonds, 21 residues, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> select add #2
7246 atoms, 7338 bonds, 929 residues, 2 models selected
> select :845-850
41 atoms, 41 bonds, 6 residues, 1 model selected
> select :1-910
7198 atoms, 7288 bonds, 928 residues, 1 model selected
> hide sel atoms
> select :acp
48 atoms, 50 bonds, 1 residue, 1 model selected
> show sel atoms
> select :ACP
48 atoms, 50 bonds, 1 residue, 1 model selected
> show sel atoms
> select ::name="ACP"
48 atoms, 50 bonds, 1 residue, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> volume #1 level 0.1108
> select sel @< 5
260 atoms, 228 bonds, 30 residues, 1 model selected
> select sel @< 5
7222 atoms, 630 bonds, 905 residues, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> select :ACP
48 atoms, 50 bonds, 1 residue, 1 model selected
> select :1-910
7198 atoms, 7288 bonds, 928 residues, 1 model selected
> hide sel atoms
> select :ACP
48 atoms, 50 bonds, 1 residue, 1 model selected
> select sel @< 5
260 atoms, 228 bonds, 30 residues, 1 model selected
> select sel @< 5
7222 atoms, 630 bonds, 905 residues, 1 model selected
> show sel atoms
> select sel :< 5
7245 atoms, 7338 bonds, 928 residues, 1 model selected
> select sel :< 5
7246 atoms, 7338 bonds, 929 residues, 1 model selected
> select :ACP
48 atoms, 50 bonds, 1 residue, 1 model selected
> select sel :< 5
463 atoms, 454 bonds, 30 residues, 1 model selected
> select :1-910
7198 atoms, 7288 bonds, 928 residues, 1 model selected
> hide sel atoms
> select :ACP
48 atoms, 50 bonds, 1 residue, 1 model selected
> select sel :< 5
463 atoms, 454 bonds, 30 residues, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> select :ACP, Mg
52 atoms, 50 bonds, 5 residues, 1 model selected
> select sel :< 5
623 atoms, 594 bonds, 54 residues, 1 model selected
> volume zone #1 nearAtoms sel & #2 range 2.0
> select :1-910
7198 atoms, 7288 bonds, 928 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select :ACP, Mg
52 atoms, 50 bonds, 5 residues, 1 model selected
> show sel atoms
> select subtract /B:1@MG
51 atoms, 50 bonds, 4 residues, 1 model selected
> hide sel atoms
> undo
> select add /B:1@MG
52 atoms, 50 bonds, 5 residues, 1 model selected
> select /B:1@MG
1 atom, 1 residue, 1 model selected
> select #1
3 models selected
> select :1-910
7198 atoms, 7288 bonds, 928 residues, 1 model selected
Drag select of 1 9ZLK.mrc , 1 atoms
> select clear
Drag select of 1 9ZLK.mrc , 48 atoms, 49 bonds
> select #1
3 models selected
> select clear
> volume hide
Drag select of 48 atoms, 49 bonds
Drag select of 49 atoms, 50 bonds
Drag select of 46 atoms, 48 bonds
> select clear
> select /B:1@MG
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select /B:2@MG
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select /B:3@MG
1 atom, 1 residue, 1 model selected
> hide sel atoms
Drag select of 49 atoms, 50 bonds
> volume zone #1 nearAtoms sel & #2 range 2.0
> volume show
> select sel :< 4
376 atoms, 366 bonds, 24 residues, 1 model selected
> show sel atoms
> volume zone #1 nearAtoms sel & #2 range 2.0
> vop resample #1 spacing 0.5
Opened 9ZLK.mrc resampled as #3, grid size 714,714,714, pixel 0.5, shown at
step 1, values float32
> volume zone #1 nearAtoms sel & #2 range 2.0
[Repeated 1 time(s)]
> volume show
> volume zone #1 nearAtoms sel & #2 range 2.0
> hide #!1 models
> show #!1 models
> hide #!3 models
> volume #1 level 0.08284
> volume zone #1 nearAtoms sel & #2 range 2.5
> select add #2
7246 atoms, 7338 bonds, 929 residues, 2 models selected
> select subtract #2
1 model selected
> select add #2
7246 atoms, 7338 bonds, 929 residues, 1 model selected
> select subtract #2
1 model selected
> lighting soft
[Repeated 1 time(s)]
> lighting simple
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting soft
> lighting simple
> graphics silhouettes true
> lighting simple
> graphics silhouettes false
> lighting simple
> volume #1 level 0.07775
> volume #1 level 0.111
> volume #1 level 0.08
> show #!3 models
> hide #!1 models
> volume zone #1 nearAtoms sel & #2 range 2.5
no atoms specified for zone
> select add #2
7246 atoms, 7338 bonds, 929 residues, 1 model selected
> volume zone #1 nearAtoms sel & #2 range 2.5
> hide #!3 models
> show #!1 models
> vop resample #1 spacing 0.5
Opened 9ZLK.mrc resampled as #4, grid size 714,714,714, pixel 0.5, shown at
step 1, values float32
> hide #!2 models
> show #!2 models
> volume zone #4 nearAtoms sel & #2 range 2.5
> hide #!4 models
> show sel atoms
> hide sel atoms
> select :ACP, Mg
52 atoms, 50 bonds, 5 residues, 1 model selected
> show sel atoms
> select /B:1@MG
1 atom, 1 residue, 1 model selected
> select /B:1@MG
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select /B:2@MG
1 atom, 1 residue, 1 model selected
> hide sel atoms
Drag select of 49 atoms, 50 bonds
> select sel :< 4
376 atoms, 366 bonds, 24 residues, 1 model selected
> show sel atoms
> volume zone #4 nearAtoms sel & #2 range 2.5
> show #!4 models
> color (#!2 & sel) gray
> color (#!2 & sel) byhetero
> color #4 #5d5d41ff models
> color #4 #646446ff models
> color #4 #70704eff models
> color #4 #bfbf85ff models
> color #4 #787854ff models
> color #4 #5b5b40ff models
> color #4 #53533aff models
> color #4 #616144ff models
> color #4 #6d6d4cff models
> view sel
> volume zone #4 nearAtoms sel & #2 range 2.
> volume zone #4 nearAtoms sel & #2 range 2.2
> volume #4 level 0.1109
> volume #4 level 0.06453
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/AMPPCP_Mg_4.png
> width 3000 height 1960 supersample 3 transparentBackground true
> color (#!2 & sel) byelement
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/AMPPCP_Mg_5.png
> width 3000 height 1960 supersample 3 transparentBackground true
> select add #2
7246 atoms, 7338 bonds, 929 residues, 2 models selected
> select subtract #2
1 model selected
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/AMPPCP_Mg_5.png
> width 3000 height 1960 supersample 3 transparentBackground true
> select :ACP, Mg
52 atoms, 50 bonds, 5 residues, 1 model selected
> select /B:3@MG
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select :ACP, Mg
52 atoms, 50 bonds, 5 residues, 1 model selected
> select sel :< 3
346 atoms, 332 bonds, 25 residues, 1 model selected
> select sel :< 6
7227 atoms, 1472 bonds, 910 residues, 1 model selected
> hide sel atoms
> select :ACP, Mg
52 atoms, 50 bonds, 5 residues, 1 model selected
> show sel atoms
> select /B:1@MG
1 atom, 1 residue, 1 model selected
> select /B:1@MG
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select /B:2@MG
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select /B:3@MG
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select sel :< 4
24 atoms, 20 bonds, 4 residues, 1 model selected
> show sel atoms
> volume #!4 hide
Drag select of 49 atoms, 50 bonds
> select sel :< 4
376 atoms, 366 bonds, 24 residues, 1 model selected
> show sel atoms
> volume zone #4 nearAtoms sel & #2 range 2.2
> show #!4 models
> volume zone #4 nearAtoms sel & #2 range 2.2
> color #4 #b0b07bff models
> color #4 #86865eff models
> color #4 #6b6b4bff models
> color #4 #55553bff models
> volume #4 step 1
> volume #4 level 0.111
> volume #4 level 0.07625
> select add #2
7246 atoms, 7338 bonds, 929 residues, 2 models selected
> select subtract #2
1 model selected
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/AMPPCP_Mg_6.png
> width 3000 height 1960 supersample 3 transparentBackground true
> volume zone #4 nearAtoms sel & #2 range 2.0
no atoms specified for zone
> select add #2
7246 atoms, 7338 bonds, 929 residues, 1 model selected
> volume zone #4 nearAtoms sel & #2 range 2.0
> select :ACP, Mg
52 atoms, 50 bonds, 5 residues, 1 model selected
> select :1-910
7198 atoms, 7288 bonds, 928 residues, 1 model selected
> hide sel atoms
> select :ACP, Mg
52 atoms, 50 bonds, 5 residues, 1 model selected
> show sel atoms
> select /B:1@MG
1 atom, 1 residue, 1 model selected
> select /B:1@MG
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select /B:2@MG
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select /B:3@MG
1 atom, 1 residue, 1 model selected
> hide sel atoms
Drag select of 49 atoms, 50 bonds
> select sel :< 3
319 atoms, 311 bonds, 19 residues, 1 model selected
> show sel atoms
> volume zone #4 nearAtoms sel & #2 range 2.0
> show #!4 models
> volume #4 level 0.111
> volume #4 level 0.08
> select add #2
7246 atoms, 7338 bonds, 929 residues, 2 models selected
> select subtract #2
1 model selected
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/AMPPCP_Mg_7.png
> width 3000 height 1960 supersample 3 transparentBackground true
> sel: 1-910
Unknown command: sel: 1-910
> show atoms
> hide atoms
> sel: 675-716
Unknown command: sel: 675-716
> show atoms
> sel: 675-716
Unknown command: sel: 675-716
> hide atoms
> sel: 675-716
Unknown command: sel: 675-716
> select :675-716
326 atoms, 330 bonds, 42 residues, 1 model selected
> show sel atoms
> volume zone #4 nearAtoms sel & #2 range 2.0
> show #!1 models
> hide #!1 models
> select :675-716
326 atoms, 330 bonds, 42 residues, 1 model selected
> hide sel atoms
> select :ACP, Mg
52 atoms, 50 bonds, 5 residues, 1 model selected
> show sel atoms
> select /B:3@MG
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select /B:1@MG
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select /B:2@MG
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select sel :< 3
9 atoms, 7 bonds, 2 residues, 1 model selected
> show sel atoms
> undo
Drag select of 49 atoms, 50 bonds
> select sel :< 3
319 atoms, 311 bonds, 19 residues, 1 model selected
> show sel atoms
> volume zone #4 nearAtoms sel & #2 range 2.0
> select add #2
7246 atoms, 7338 bonds, 929 residues, 2 models selected
> select subtract #2
1 model selected
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/AMPPCP_4.png width
> 3000 height 1960 supersample 3 transparentBackground true
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/AMPPCP_Mg_2.cxs
> includeMaps true
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 912, 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 641, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX\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\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\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\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display
run(session, cmd)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\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\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 912, 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 641, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX\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.
> save C:/Users/mbash/OneDrive/Desktop/MgtA_paper/TMs_Maps/AMPPCP_Mg_2.cxs
> includeMaps true
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 912, 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 641, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX\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\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\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\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display
run(session, cmd)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\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\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 912, 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 641, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX\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: 3.3.0 NVIDIA 581.04
OpenGL renderer: NVIDIA GeForce RTX 3060/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.2
Locale: en_CA.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows
Manufacturer: Dell Inc.
Model: XPS 8950
OS: Microsoft Windows 11 Home (Build 26200)
Memory: 16,890,650,624
MaxProcessMemory: 137,438,953,344
CPU: 20 12th Gen Intel(R) Core(TM) i7-12700
OSLanguage: en-US
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.1
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.22.3
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.7
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.13
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.3
ChimeraX-PDBMatrices: 1.0
ChimeraX-PhenixUI: 1.2.1
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.2
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.0
comtypes: 1.1.14
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.0
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.5.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.8
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 23.2
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pickleshare: 0.7.5
Pillow: 10.0.1
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pywin32: 305
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.7
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.5
sphinxcontrib-htmlhelp: 2.0.4
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.6
sphinxcontrib-serializinghtml: 1.1.9
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.3
urllib3: 2.1.0
wcwidth: 0.2.12
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
WMI: 1.5.1
Change History (2)
comment:1 by , 10 days ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Sessions |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → MemoryError saving session with maps |
comment:2 by , 10 days ago
| Resolution: | → limitation |
|---|---|
| Status: | assigned → closed |
The ChimeraX error message saving a session means it ran out of memory. The bug report does not show how big your maps and models were. You were saving a session with the "include maps in the session file". Density maps can be very large so the default in ChimeraX sessions is to not include the map data, but only include a path to the original file which the session will reopen. You can probably avoid the out of memory error by not including the map data in the sessions.
You are also using an older ChimeraX version 1.7 on Windows and there was an older ChimeraX (don't recall which version) that used excessive memory. So just updating to the current ChimeraX might fix this out of memory problem.
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Reported by Muhammad